It seems to me that it's not a bug, I just restarted and everything is still wrong... On the other hand, the part I want to leave in place, I can put it back thanks to the "restore neutral position" function. But that doesn't explain why it shifts following the translation of the screw....
After several tests, you should not select 2 pieces, but only the part you want to move. Then you just have to select the Align function, then the starting axis and finally the reference axis.