As mentioned in https://github.com/syncthing/syncthing/issues/1253, I was getting tons of those messages. I have now reset the index (by removing the “index” directory in ~/.config/syncthing) and waiting for rescan (could take a couple of hours).
I will keep this thread posted if this resolves the problem. just in case someone else has the same.
Thanks to @AudriusButkevicius for the help so far.