The icon disappearing for a brief moment is because when an update is
being installed, the old desktop file is removed, then the new one is
installed, so there's an interval of time during which there is no
desktop file. That's unfortunate, but harmless.
The other problem you describe is bug #1616650: the chromium snap is
being refreshed while it is running, causing problems with the versioned
profile directory. I suggest you enable the refresh app awareness
experimental feature, which will prevent this from happening:
snap set core experimental.refresh-app-awareness=true
(see https://forum.snapcraft.io/t/wip-refresh-app-awareness/10736 for
details)
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https://bugs.launchpad.net/bugs/1851490
Title:
[snap] Favourite entry for chromium disappears with every update
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