Please make a new WIndows user and log into Windows as that. Install and run the game from there, does it still get this problem?
I don't want to make a new Windows unless absolutely necessary, so I installed process monitor and looked at the results of the syscalls involving the sqlite file. Hopefully, it is helpful.
There was one write to journal of 512 bytes, which was successful. Subsequently, the application readback some of the data written successfully. The journal file was then deleted, seemingly without any attempt to write any data to the main sqlite file.
I noticed that most of the calls to CreateFile referencing launcher-v2.sqlite-wal and launcher-v2.sqlite-journal resulted in NAME NOT FOUND. All of the these calls had the Open Reparse Point option. CreateFile calls without the Reparse Point option all seemed to succeed.
QueryAttributeTagFile on the journal failed with INVALID PARAMETER. FlushBuffersFile on the journal returned 0xC00000D2.
The single attempt to open launcher-v2.sqlit with the Open Reparse Point option also gave NAME NOT FOUND. All other operations involving the file returned SUCCESS or END OF FILE (for reads). No writes were attempted.
Edit: All the file queries returned standard stuff. Allocation size 64K, size 0 (for the main db file), size 512 (for the journal file after the write), number of links 1, not a directory.
Edit2: Reverting back to version 2.0.4.0 (from EU4 1.30.6) still fixes the problem.