Just to summarize, here are the issues I was able to reliably reproduce while doing the extensive work of cleaning up the mess sync made of my vaults this past weekend.
It’s clear to me that there was some server side issue with that zip file, and it makes me concerned for the integrity of others archives and large files in my vault. I believe there was possibly more, but in addition to trying to document what I could despite logging failures, I was focused on salvaging what I could.
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There is a very clear lack of good logging practices which would help us to run root cause analysis.
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Pause or unpause is not reliably logged in the logs that do exist (see previous posts and uploaded logs).
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Logging is unpredictable and seems to fail or delete logs without explanation in active sessions (and are not saved persistently anywhere that I found. See: Obsidian Sync: Persistent / Save Sync logs for debugging )
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It appears that sync is not using a transaction log with tombestones, or there are bugs in whatever log Obsidian is using.
I recommend anyone running sync with their vaults take regular backups. A git repo would be useful, but if you store images or other files in your vault, you may need to do so locally rather than on github.
***I strongly advise that users DO NOT RELY EXCLUSIVELY ON SYNC FOR YOUR DATA INTEGRITY.
It attempts to synchronize data between devices, at the occasional cost of data integrity, and the built in recovery tools are not easily searchable or useable for this usecase without good persistent logs.***