Let me see if I can puzzle out what “lost” means, or please clarify rather than throwing it in double quotes.
In this topic, manifest files suddenly jumped in yesterday. Manifest files are never standalone files deleted from destination the way a dblock, dindex, or dlist file would be. They’re a file included in all such file types. The other topic where you mentioned manifest also showed one here without any explanation about “lost”.
Sorry, I have no idea why you’re pointing to manifest files. Do you see a manifest file problem or a problem with some other type of file? Got error messages? Got logs? Got the time history of what happened when?
Repair should never recreate a manifest file without a containing file, and compact should never delete one. These are internal files. Have you found a problem at the file internals level, or is it a dblock/dindex problem which seems more likely based on the known issues? You can view a log file (live log is fine) for file names.
Repair also has a limited ability to recreate destination files. It can do dindex and dlist, but dblock is tougher.
If you kept a better log file, look in it. See if you see a complaint with “Missing file” in its text. If there is some history from the previous backup, post that to show how it ended. Issue might be found on the next backup.
If you see a manifest file named in your log, please post it. I don’t think you will though. They’re internal files.
Have you been leaving the problem system alone or already done things to it? A look by you (or bug report) would have been nice. If system has been left alone, please copy the DB or get a DB bug report snapshot. Saved log files are a more reliable view, but go well with a DB snapshot to look for inconsistencies such as dindex file actual delete that the DB then forgets about by rollback. That open issue was referenced before.