So we recently lost 5 of our 20 trade pacts, and I'm not quite sure why. Admittedly I don't follow up on the legions we keep trade pacts with, so the only thing I could think of is that they were inactive and recently purged. Seems strange to lose 5 pacts overnight though with no notice. Anyone know what could cause this?

This doesn't seem like an in game issue.
You admit to not really following it so it is most likely that the pacts were broken and you didn't notice.

Unless maybe your base didn't have enough upkeep???

We have plenty for upkeep, I meant I don't keep up on the legions themselves (not the pacts), and we have no recently broken pacts to review. No other officers saw and/or dismissed any notices either. We had 20 last night when I buffed, 15 this afternoon when I checked.

Question, do you have 5 empty spots in your Diplomacy tab?

Because if your Mission Control Center was just installed maybe an Embassy was taken out to make room.

We recently refilled the pact slots, but no embassies were removed or re-added. We added the special extenders to add the mission control module earlier in the week.