SUMMARY
I noticed that when upgrading (or just editing) books in calibre, they somehow lose the ability to have a thumbnail (in dolphin) generated and are just the generic file attribute cover for a ".epub" file

STEPS TO REPRODUCE
1. have a EPUB(2) file that has a cover *before* adding to calibre
2. import original EPUB file into calibre (any latest version)
3. open "Edit book" in calibre on the imported epub
4. select "Tools -> Upgrade book internals" to upgrade the file to EPUB3
5. save the edited book
6. go to the directory where the file is (in the calibre library), in my case with dolphin
7. observe not having a cover

OBSERVED RESULT
Generic file attribute thumbnail for edited file in calibre

EXPECTED RESULT
Thumbnail from the EPUB cover

SOFTWARE/OS VERSIONS
Operating System: Manjaro Linux
KDE Plasma Version: 5.24.3
KDE Frameworks Version: 5.91.0
Qt Version: 5.15.3
Kernel Version: 5.16.14-1-MANJARO (64-bit)
Graphics Platform: Wayland
Processors: 8 × Intel® Core™ i7-7700K CPU @ 4.20GHz
Memory: 31.3 GiB of RAM
Graphics Processor: AMD Radeon RX Vega

ADDITIONAL INFORMATION
The most consistent way to reproduce this problem is to have a EPUB2 file upgraded to a EPUB3 file, but it also happens when applying other changes (though i could not to consistently reproduce it with something else)

this issue might be similar to https://bugs.kde.org/show_bug.cgi?id=451226, but that one seems to be fixed

in my case calibre is installed as a flatpak as version 5.40.0 

from what i can tell from my testing, all EPUB3's that *dont* have "manifest -> item -> cover -> properties="cover-image"" set, just work, all others that either have that set or reference it with "metadata -> meta -> cover -> content="cover-image"" (where "content="id"" is the id set in manifest) dont work