I suspect that might have something to do with the problem (some memory overflow possibly?)? Anyway, I can NOT reproduce the error now. My unfortunate erroneous sync was done after a longer period so I had several thousands files marked for syncing. Note: The compare task is quite big, having ~300.000 files and ~300+GB data. So, it is very strange and finding the source of the bug is not easy. I use still the same sync setting, no change here.
Now, to increase confusion - I tried again 11.12 and it seems OK - at least on my current disk status I can not repeat the previous error. But it was done after my restore, so the original state of files on disk is different now. I have restored most (all?) of my rewritten files from backups, but it was really unpleasant experience. OK, maybe just for me, but the update to 11.12 was a total disaster.
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