Ok I just updated to 9.5.30 an got the same message!
I created a new instrumental from scratch using the hiphop template in the hub menu just to test out the new update!
I think the issue does have something to do with the pool /trash can an the amount of changes you make within the project! I do a lot of copy an paste with ctrl/k!
Also how many here have there cloud storage services connected to there song files folder an when I close the session then quit cubase I get a notification from Google drive about changes made to the song an if I want to do this or that but I exit out! Didn’t have any issues coming from 8.5 or cb 9 using the same cloud computing an also use reason an Abelton an no issues while working on music then automatically backing up to the cloud!
As far as saving the song ,the message just disappeared after making a patch change, saved with ctrl/S , ctrl/w to quit session an ctrl/Q to exit cubase ,poop crazy, lol