this is expected behaviour under the freedesktop XDG specification and does not
at all differ from how deb packages handle .desktop packages in
/usr/share/applications (just that snapd puts these files in their own location
where the XDG system reads them).
these files are package-owned and will always be replaced by design.
to override the package-owned files the XDG specification provides the
~/.local/share/applications/ directory. copy the package-shipped files like:
cp /var/lib/snapd/desktop/applications/spotify_spotify.desktop \
~/.local/share/applications/
then you are free to edit the file in ~/.local/share/applications/ to
your needs and it will not be overwritten (and will be preferred over
the one shipped in the package).
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https://bugs.launchpad.net/bugs/1799321
Title:
customization of desktop files overwritten when snaps are updated
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