The syntax of the Exec command in the export .desktop file is wrong, and should be Exec=/usr/bin/flatpak run --branch=main --arch=aarch64 --command=axolotl org.nanuc.Axolotl -axolotlWebDir=/app/bin/axolotl-web/dist -e=qt
The syntax of the Exec command in the files .desktop file should be Exec=axolotl -axolotlWebDir=/app/bin/axolotl-web/dist -e=qt
At least for the recent qt merge, there are two .desktop files, one in export and one in files:
/home/mobian/flatpak/app/org.nanuc.Axolotl/aarch64/main/b49374dab17751c5bfa617ccae1c3c18335c3876068ddb9d1fab4efe2f5a1f60/export/share/applications/org.nanuc.Axolotl.desktop
/home/mobian/flatpak/app/org.nanuc.Axolotl/aarch64/main/b49374dab17751c5bfa617ccae1c3c18335c3876068ddb9d1fab4efe2f5a1f60/files/share/applications/org.nanuc.Axolotl.desktop
The syntax of the Exec command in the export .desktop file is wrong, and should be
Exec=/usr/bin/flatpak run --branch=main --arch=aarch64 --command=axolotl org.nanuc.Axolotl -axolotlWebDir=/app/bin/axolotl-web/dist -e=qt
The syntax of the Exec command in the files .desktop file should be
Exec=axolotl -axolotlWebDir=/app/bin/axolotl-web/dist -e=qt