Not sure if it helps to track down the problem but here are some issues I tracked down:
I’m using Logseq on a laptop and a desktop, both Ubuntu 22.04, both syncing to Nextcloud via the Nextcloud Desktop app.
I also use it on an Android 8.1 phone and an Android 10 tablet, both using Folder Sync Pro via WebDAV.
First, both of my computers are running for long hours every day. Especially my laptop - it’s old, so I don’t shut it down for breaks. I noticed that the Nextcloud Desktop client doesn’t seem to like to run for a long time nonstop and somehow goes haywire and either doesn’t sync or syncs some BS. I opened a Github issue for the client here: [Bug]: Client stops syncing files after a while and goes haywire. · Issue #5891 · nextcloud/desktop · GitHub
Second, although configured to sync deletions, Folder Sync Pro seems to skip to sync down file deletions sometimes. Sync down meaning, a file was deleted on the server and FSP should delete it on the phone too. That I could verify. I’m keeping a close eye on that (and Nextcloud sync) now to locate any other potential problems.