diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4994e0660..92d282ac4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Fixed
+
+- added a missing implementation for a branch in `Grid::merge` that was
+  triggered when exporting some PineAPPL grids generated from the 'pinejet'
+  group
+- fixed wrong coupling orders when exporting to APPLgrid. This happened when
+  the PineAPPL grid had orders that had any other ordering than 'LO', 'NLO',
+  'NNLO'
+- fixed a bug that caused exported grids to compare unsuccessfully when the
+  convolution functions were proton-anti-proton; APPLgrid doesn't store the
+  types of convolution functions, so we simply convert the grid to use only
+  proton PDFs
+
 ## [1.1.0] - 08/07/2025
 
 ### Added
diff --git a/maintainer/test-cli-export.sh b/maintainer/test-cli-export.sh
new file mode 100755
index 000000000..c1afbb059
--- /dev/null
+++ b/maintainer/test-cli-export.sh
@@ -0,0 +1,66 @@
+#!/bin/bash -x
+
+set -euo pipefail
+
+grids=(
+    ## Ploughshare
+
+    # Group: pinejet
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-atlas-wm-arxiv-1109.5141/pinejet-atlas-wm-arxiv-1109.5141.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-atlas-wm-arxiv-1603.09222/pinejet-atlas-wm-arxiv-1603.09222.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-atlas-wm-arxiv-1612.03016/pinejet-atlas-wm-arxiv-1612.03016.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-atlas-wp-arxiv-1109.5141/pinejet-atlas-wp-arxiv-1109.5141.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-atlas-wp-arxiv-1603.09222/pinejet-atlas-wp-arxiv-1603.09222.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-atlas-wp-arxiv-1612.03016/pinejet-atlas-wp-arxiv-1612.03016.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-atlas-z0-arxiv-1109.5141/pinejet-atlas-z0-arxiv-1109.5141.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-atlas-z0-arxiv-1305.4192/pinejet-atlas-z0-arxiv-1305.4192.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-atlas-z0-arxiv-1404.1212/pinejet-atlas-z0-arxiv-1404.1212.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-atlas-z0-arxiv-1603.09222/pinejet-atlas-z0-arxiv-1603.09222.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-atlas-z0-arxiv-1606.01736/pinejet-atlas-z0-arxiv-1606.01736.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-atlas-z0-arxiv-1612.03016/pinejet-atlas-z0-arxiv-1612.03016.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-atlas-z0-arxiv-1710.05167/pinejet-atlas-z0-arxiv-1710.05167.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-cdf-z0-arxiv-0908.3914/pinejet-cdf-z0-arxiv-0908.3914.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-cms-wm-arxiv-1206.2598/pinejet-cms-wm-arxiv-1206.2598.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-cms-wm-arxiv-1312.6283/pinejet-cms-wm-arxiv-1312.6283.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-cms-wm-arxiv-1603.01803/pinejet-cms-wm-arxiv-1603.01803.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-cms-wp-arxiv-1206.2598/pinejet-cms-wp-arxiv-1206.2598.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-cms-wp-arxiv-1312.6283/pinejet-cms-wp-arxiv-1312.6283.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-cms-wp-arxiv-1603.01803/pinejet-cms-wp-arxiv-1603.01803.tgz"
+    #"https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-cms-z0-arxiv-1310.7291/pinejet-cms-z0-arxiv-1310.7291.tgz" # fails due to static-scale optimization
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-d0-wm-arxiv-1309.2591/pinejet-d0-wm-arxiv-1309.2591.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-d0-wp-arxiv-1309.2591/pinejet-d0-wp-arxiv-1309.2591.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-d0-z0-arxiv-0702025/pinejet-d0-z0-arxiv-0702025.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-lhcb-wm-arxiv-1505.07024/pinejet-lhcb-wm-arxiv-1505.07024.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-lhcb-wm-arxiv-1511.08039/pinejet-lhcb-wm-arxiv-1511.08039.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-lhcb-wp-arxiv-1505.07024/pinejet-lhcb-wp-arxiv-1505.07024.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-lhcb-wp-arxiv-1511.08039/pinejet-lhcb-wp-arxiv-1511.08039.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-lhcb-z0-arxiv-1505.07024/pinejet-lhcb-z0-arxiv-1505.07024.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-lhcb-z0-arxiv-1511.08039/pinejet-lhcb-z0-arxiv-1511.08039.tgz"
+    "https://ploughshare.web.cern.ch/ploughshare/db/pinejet/pinejet-lhcb-z0-arxiv-1607.06495/pinejet-lhcb-z0-arxiv-1607.06495.tgz"
+)
+
+tmp=$(mktemp -d)
+cd "${tmp}"
+
+trap "cd && rm -rf ${tmp}" EXIT SIGKILL
+
+for grid in ${grids[@]}; do
+    archive=${grid##*/}
+    wget --no-verbose --no-clobber "${grid}" -O /tmp/"${archive}" || true
+    mkdir subdir
+    tar xzf /tmp/"${archive}" -C subdir
+
+    for grid in $(find subdir \( -name '*.lz4' \)); do
+        if [[ $(basename $grid) =~ ^\..* ]]; then
+            continue
+        fi
+
+        converted_grid="${grid}".appl
+        reimported_grid="${grid}".new.pineappl.lz4
+        pineappl export --accuracy 1e-12 "${grid}" "${converted_grid}" NNPDF31_nnlo_as_0118_luxqed
+        pineappl import --accuracy 1e-12 "${converted_grid}" "${reimported_grid}" NNPDF31_nnlo_as_0118_luxqed
+        du -h "${converted_grid}" "${reimported_grid}"
+    done
+
+    rm -r subdir
+done
diff --git a/pineappl/src/grid.rs b/pineappl/src/grid.rs
index 48d2d84e4..82244a6c9 100644
--- a/pineappl/src/grid.rs
+++ b/pineappl/src/grid.rs
@@ -944,17 +944,8 @@ impl Grid {
                     .multi_slice_mut((s![.., .., index], s![.., .., other_index]));
 
                 for (lhs, rhs) in a.iter_mut().zip(b.iter_mut()) {
-                    if !rhs.is_empty() {
-                        if lhs.is_empty() {
-                            // we can't merge into an EmptySubgridV1
-                            *lhs = mem::replace(rhs, EmptySubgridV1.into());
-                            // transpose `lhs`
-                            todo!();
-                        } else {
-                            lhs.merge(rhs, Some((a_subgrid, b_subgrid)));
-                            *rhs = EmptySubgridV1.into();
-                        }
-                    }
+                    lhs.merge(rhs, Some((a_subgrid, b_subgrid)));
+                    *rhs = EmptySubgridV1.into();
                 }
             }
         }
diff --git a/pineappl/src/subgrid.rs b/pineappl/src/subgrid.rs
index 799bb51ae..d575abaaf 100644
--- a/pineappl/src/subgrid.rs
+++ b/pineappl/src/subgrid.rs
@@ -418,15 +418,21 @@ impl SubgridEnum {
         if other.is_empty() {
             return;
         }
+
         if let Self::EmptySubgridV1(_) = self {
-            if transpose.is_none() {
+            if transpose.is_some() {
+                // change the type of `self` to the type of `other`
                 *self = other.clone();
+                // TODO: emptying `self` could be done more efficiently, we're probably storing a
+                // lot of zeros here
+                self.scale(0.0);
             } else {
-                todo!();
+                *self = other.clone();
+                return;
             }
-        } else {
-            self.merge_impl(other, transpose);
         }
+
+        self.merge_impl(other, transpose);
     }
 }
 
diff --git a/pineappl_cli/src/export/applgrid.rs b/pineappl_cli/src/export/applgrid.rs
index 109c9c098..a251a062b 100644
--- a/pineappl_cli/src/export/applgrid.rs
+++ b/pineappl_cli/src/export/applgrid.rs
@@ -111,8 +111,19 @@ pub fn convert_into_applgrid(
         bail!("grid has non-consecutive bin limits, which APPLgrid does not support");
     }
 
-    if grid.convolutions().len() > 2 {
-        bail!("APPLgrid does not support grids with more than two convolutions");
+    match grid.convolutions() {
+        [_] => {}
+        [a, b] => {
+            if a != b {
+                if a.cc() == *b {
+                    // use charge conjugate to map hadron-anti-hadron grids to use the same single
+                    // convolution function
+                    let index = if a.pid() < 0 { 0 } else { 1 };
+                    grid.charge_conjugate(index);
+                }
+            }
+        }
+        _ => bail!("APPLgrid does not support grids with more than two convolutions"),
     }
 
     // APPLgrid only understands PDG PIDs
@@ -156,9 +167,11 @@ pub fn convert_into_applgrid(
         .collect();
 
     // `id` must end with '.config' for APPLgrid to know its type is `lumi_pdf`
-    let id = "PineAPPL-Lumi.config";
+    let id = format!("{}.config", output.file_stem()
+        // UNWRAP: because we write to that file in the end, there always must be a file name
+        .unwrap().to_string_lossy());
     // this object is managed by APPLgrid internally
-    ffi::make_lumi_pdf(id, &combinations).into_raw();
+    ffi::make_lumi_pdf(&id, &combinations).into_raw();
 
     let limits: Vec<_> = grid
         .bwfl()
@@ -200,17 +213,17 @@ pub fn convert_into_applgrid(
         - lo_alphas;
 
     let mut applgrid =
-        ffi::make_empty_grid(&limits, id, lo_alphas.into(), loops.into(), "f2", "h0");
+        ffi::make_empty_grid(&limits, &id, lo_alphas.into(), loops.into(), "f2", "h0");
 
-    let has_pdf1 = !grid.convolutions().is_empty();
-    let has_pdf2 = grid.convolutions().get(1).is_some();
+    // APPLgrid has either two or one convolution(s)
+    let convolutions = grid.convolutions().len();
 
-    for (appl_order, order) in order_mask
+    for order in order_mask
         .iter()
         .enumerate()
         .filter_map(|(index, keep)| keep.then_some(index))
-        .enumerate()
     {
+        let appl_order = grid.orders()[order].alphas - lo_alphas;
         let factor = TAU.powi(grid.orders()[order].alphas.into());
 
         for (bin, subgrids) in grid
@@ -275,9 +288,7 @@ pub fn convert_into_applgrid(
                     })
                     .collect::<Result<_>>()?;
 
-                // in the DIS case APPLgrid always uses the first x dimension
-
-                let (x1_grid, x2_grid) = if has_pdf1 && has_pdf2 {
+                let (x1_grid, x2_grid) = if convolutions == 2 {
                     (
                         grid.kinematics()
                             .iter()
@@ -298,26 +309,13 @@ pub fn convert_into_applgrid(
                             // TODO: convert this into an error
                             .unwrap(),
                     )
-                } else if has_pdf1 {
-                    (
-                        grid.kinematics()
-                            .iter()
-                            .zip(subgrid.node_values())
-                            .find_map(|(kin, node_values)| {
-                                matches!(kin, &Kinematics::X(idx) if idx == 0)
-                                    .then_some(node_values)
-                            })
-                            // TODO: convert this into an error
-                            .unwrap(),
-                        Vec::new(),
-                    )
                 } else {
                     (
                         grid.kinematics()
                             .iter()
                             .zip(subgrid.node_values())
                             .find_map(|(kin, node_values)| {
-                                matches!(kin, &Kinematics::X(idx) if idx == 1)
+                                matches!(kin, &Kinematics::X(idx) if idx == 0)
                                     .then_some(node_values)
                             })
                             // TODO: convert this into an error
@@ -376,7 +374,7 @@ pub fn convert_into_applgrid(
                         weightgrid.as_mut(),
                         appl_q2_idx,
                         appl_x1_idx[indices[1]],
-                        if has_pdf1 && has_pdf2 {
+                        if convolutions == 2 {
                             appl_x2_idx[indices[2]]
                         } else {
                             0