Literally seems to be fixed in today's update.
I just lost 750 cycles of progress because of this. At the end of my gaming session I always press "Save", select the latest autosave, and press "Overwrite", as the autosave already had a suitable name and I didn't need to come up with a new one. Yesterday I started a new colony to test some things. I come back to the old one - all my saves are gone, because the autosaves of the new colony overwrote all the old ones. Manual saves should not be treated as autosaves even if they overwrite autosaves. Users should either be unable to overwrite autosaves as this sort of manual save does not behave as expected (e.g. hide autosaves from UI when saving), or overwritten autosaves should be treated as manual saves.