Comment 8 for bug 1851490

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)