@Ushas - well spotted concerning the auto saves. I'm pretty sure that's how I'd set it up, (and subsequently forgotten) with no autosave before ally missions. Good suggestions, will look at this for V16.
@Nomad - In the region of 3 weeks, I'd say. No need to restart, but would be curious if you just did the ally missions in a row, without doing other missions, as combined with Ushas' observations, that would explain the problem.