hello @mklemme welcome to the forum 
it’s hard to say how the issue manifested. there must have been more moving parts as you description doesn’t really fit the issue.
- if you have extra files into the fie system (rsync without deleting) this files don’t appear on the system at all… they sit around on the storage and consume space but they don’t appear inside of the application… until you reindex the storage using e.g.
occ files:scancommand - but this would not create duplicate records in the DB
oc_filecachetable… likely file location is different somehow which results in new file ID - “duplicate” files in the oc_filecache table must be different from the application point of view e.g. other mount ID or something else…
- this is the reason why the share doesn’t work - when the system looks for the “initial” files it doesn’t find it… when you replace the ID of the file in the share it points to right location again…
It’s hard to say how you can recover from the issue. If you can I would recommend you to return to some working backup and start over from there. If you can’t return to a backup try to understand the issue and repair the DB (definitely not the simplest task). You might find scripts and SQL queries from this topic useful (review the whole topic there are tons of different approaches and references) Desktop client 3.4.0 destroys local time stamp and keeps uploading data to server… there was different focus but might help you at least on the files side…