Okay, found another thread after trying to figure this out. https://forums.plex.tv/t/database-repair-error-no-such-collation-sequence-icu-root/715808/6 which helped. I had to open the container shell within portainer, and run the sqlite commands from within the container.
I had to run repair to .dump and rebuild. which worked. Agree with the people in that thread, documentation should definitely be updated.
