I have definite issues with dust particles changing position, even suddenly appearing or disappearing between sessions. However, I attribute that to the fact that I am using an 'open-tube' OTA (as opposed to the likes of a Schmitt-Cassegrain or Maksutov-Cassegrain).
So, I feel that the extra effort to acquire Flats at the end of every imaging session is worthwhile. But, as always, different folk will encounter different issues.
I can agree with you about focus positions and Flats though - all other things being equal, then an optical train returned to the same focal position should require the same Flats for calibration purposes. But, if you are doing things like rotating filters in a filter-wheel, I would not be surprised to see dust particles move on the filters during that process. To me, that would require renewed Flats.