Saved project is altered by opening file in another instance

I had a project where I altered the speed of a digital version of a track to align with a vinyl rendering of a track. This was painstaking work involving the identification of the beginnings of beats at regular intervals and splitting the tracks and altering their speeds at points right before the beats, to minimize distortions.

I wanted to experiment with a different approach the next day and without opening the earlier aup3 file I right-clicked the audio file and used “Open With Audacity”. I fooled around for a bit, then closed it. When I opened my aup3 from the day before, instead of the track being aligned from the position where I started altering the speeds, the entire track was put in place. I did not touch or alter the aup3 file in any way after concluding my work the previous day. Left is how it was last evening, right is how it was this morning when I opened it.

On the top track, I also can’t move any of the split sections and attempting to skyrockets my CPU usage without doing anything.