Synchronization of information is one of the difficult problems in computing, so I’m not surprised of these issues.
I’m personally moving from Joplin not only because of the superior knowledge management LogSeq offers but also because their synchronization methods are failing on my case (I have more than 5000 references, it gets confusing).
I’m perfectly happy using git for commit-push for external storage, and pull-commit-push for synchronization with a second computer and advise anyone, even if using another method, to use git as a means to fast data recovery.