Had a sudden thought… I tried saving my problem project (which was still taking exactly 50 secs to do a save) out to a whole new project using Create Backup Project. That also copied across all the audio that was in use.
Open the new backup project and it does saves in 10 seconds. It still beachballs, but doesn’t beachball for anything like as long.
That might be a temporary solution for some of you?
Still doesn’t explain why the other project I made saves in only 1s or so. But getting closer.