Hi @HenrikPLind
Indexing your own StorageDirectory looks very weird to me and the behaviour might be unpredictable.
As you might have seen, we have just released a new advanced storage plugin that should facilitate this type of migration (full documentation).
Your migration scenario has been described in this Docker setup (you can just reuse the configurations on Windows).
If I understand correctly, you would now have 2 “old storages”, the initial SQLite one and the one for PG that has already received some data → you should therefore start another Orthanc instance with the new plugin and yet another empty StorageDirectory and index these 2 “old” folders.
Hope this helps,
Alain.