I keep getting syncing: no connected device has the required version of this file for some few files that should already be deleted and/or are not relevant.
Now it keeps recreating empty folders as it anticipates those files.
Can I somehow tell syncthing to stop caring about these files?
Not really. It’s possible that that the file might have neen modified by some (now offline) device as it has been deleted on some other one, and the modification wins over the deletion, so it’s trying to sync that.
The way to recover from this is to re-create the file (can be empty), let that sync, and then delete it, or bring back the offline device that modified the file as it was deleted.
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