What at least helped in my case, was stopping the backup, stopping the service, opening the database with an SQLITE editor (e.g. DB Browser for SQL Lite) and running the sql command ANALYZE.
Afterwards all SELECTS and stuff were running in a reasonable time.
This might also be a hint for the developers how to fix this. I had the same issue also with recreating a database (Queries running sometimes for 3-4 days). Maybe this could generally solve the slow access on the database.