I asked Kovid in PM if cal6 ever deletes the contents of resources/images, he said, "yes, when migrating legacy icon themes. That is if you have a icon-theme.json in that folder."
So it makes sense that some of us (who didn't use icon themes in cal5) wouldn't see this issue.
Since it's only while migrating, it shouldn't be an ongoing issue once you've switched to cal6.
Changing where GC keeps its images is easy--migrating them for existing users is less easy. Should it be automatic and silent? Or inform/ask the user? Under calibre\plugins is the obvious new place.
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