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There's a few of things I can suggest.
1) In your custom .desktop file, make the Name entry something like Sigil AppImage. That way it will stand out from any other installed versions something like:
Name=Sigil AppImage
2) try the full path to your home directory rather than using the ~
/home/(username)/
3) See if your distro has the desktop-file-validate tool available. If it does, install it if necessary and run:
desktop-file-validate ~/.local/share/applications/sigil.desktop (or whatever your desktop file is named) and make sure is doesn't show any errors in your .desktop file.
4) make sure the executable bit is set on your .desktop file.
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