I've been encountering an issue (which is probably more of a Windows issue?) with certain albums where the metadata will "erase" itself from being displayed in Windows File Explorer after pasting updated Artwork in MP3Tag.
I've gotten to the point where this is re-creatable with certain types of artwork. It seems like the artwork image is more of the cause than the flac's themselves. I have an example below:
Looks like your explorer does not recognize the files to be audio files.
The second window does not show the (yellow) "Play" ribbon header.
And the location for the files seems to be different, looking at the 2 types of icons.
The example file has a really large embedded picture, it's 3MB which breaks Windows Explorer.
If you remove it or resize it from within Mp3tag (e.g., via Adjust Cover), the preoccupied space is still left as padding (which is reserved space for future changes). Unfortunately, it might be still too large for Explorer to handle.
Before you ask: removal of padding (or at least resizing it to something that makes sense) is on my internal list of things to improve for Mp3tag. Until then, you can create this workaround using metaflac.exe (you can download it from the FLAC website, look for flac-1.4.2-win.zip).
In Mp3tag, define a user-defined tool via Options → Tools, and name it, e.g., FLAC remove padding, put the path to metaflac.exe and use the parameters