New user, starting out in Studio One 5 Pro (Sphere, actually). Just ran into very similar problems like this today, on my first chunk of finished work in S1, so my first attempt at using the much-hyped Song <> Project update workflow.
Let's just say when you manage to shake the beverage dispenser several times and finally hit the thing hard enough, it finally works and it works well. But the basic, bread-and-butter "Update Mastering File" workflow is terribad and bug-prone. I found myself needing to literally copy my song-specific mastering inserts into the "Mastering" section so that I could literally delete the existing song in the project, then go over to the song page and do the "update mastering file" from there, and then come back into the Project page and re-import the .song file again and set up everything again on that new instance of the song in the project: offset inside the track, fades, moving inserts back into the track-specific section.
It was a frustrating experience. I had to go through this process usually two-three times PER SONG ITERATION to get the latest small song changes to actually sit properly in the Project with no issues.
The biggest--and most alarming--issue I keep running into is a song file (in the Project) that would have a random dropout. That dropout did NOT exist in the song, but it would be there in the project until I did the delete-and-reload manually dance. Another time I had the song all set up right and looking good, but then went back to the Song to make one small change, and the "update mastering file" caused a regular set of complete dropouts literally every 16 bars, like clockwork, right on the downbeat of every bar. Again, nothing at all like that in the Song file. The Song file was perfect. The only fix was the blow away the song track in the Project and once again do everything all over again.
Note that in one case you could not SEE the dropout in the waveform in the Project, but you could certainly hear it and see in any type of oscilloscope display of the song as it played past that point in the timeline. In other cases, though (like the big dropouts every 16 bars like clockwork), you could actually SEE the dropout sections in the waveform in the Project.
I can see how y'all are frustrated by this. It's supposed to be a major workflow feature of S1, but it's unreliable as heck.
FWIW, I'm on a beefy Windows 10 system and Studio One Pro 5 is generally working well, but at this point I'm already reconsidering my Sphere subscription and whether to stick with S1 or keep looking.