Ok, so I was a happy man for a day, but hey, happiness cannot last long. Now Synchthing Tray cannot connect to the Synchthing service and boils the CPU. The service works fine in the background, though.
Correction to my original question: the mentioned /workspace partition has NTFS file system (the system partition is btrfs), since I dual-boot Windows and Linux. Maybe that was the root cause.
Seems like I will have convert the /workspace to btrfs anyway, because Linux software does not handle it well due to difference in permissions models.