He probably deleted the expired aid's record, because it had, y'know, expired. Doing that would remove the record of the aid from both his and your aid screen. Simple, really.
For a trade to have the team bonus, you have to be on the same team for the entire duration for the trade.
You'll have to cancel and resend trade offers.
There's no "processing" involved in resources. You simply have resources that give you (usually beneficial) effects, and trading means that you have more resources, so more effects (except for copies of the same resources). The advantage of trading is that you get the effects of another nation's resources.
Does he have an event which disables affluent population? There are a few different ones that do this. If so, he'll get AP back once the event expires.