You can try reaching out to ente directly. They've been pretty responsive in the past even though I'm also self hosting.
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I was a bit unsure of contacting them because of self hosting it. Thanks for telling me! I'll edit the post to add the fix if I/they found a way to resolve it.
Before you redo the rest by hand, check whether the broken ones share a format. Black frames that render fine on the phones but not in a desktop browser usually mean the original file is intact and it was the server-side preview that failed to generate, with the phones quietly decoding the original themselves. HEIC and HEVC and 10-bit HDR are the usual suspects, since those lean on libheif and ffmpeg on the server and older builds choke on them.
If that's the cause, re-uploading only "works" because it reruns preview generation, so you're really just triggering a fresh encode. Grep the museum logs around one of the bad files for a decode error, and see whether a rescan or clearing the thumbnail cache regenerates them in place. That would save you doing the whole library one file at a time.
Does the issue only occour for live photos? If so it might also be an issue with video codecs 🤷♂️.