So, started playing this morning, before the switch prompt. When the switch option happened (and we were all ported to whatever base), I talked to Maria Hill (I was Pro), cleared all her prompts or whatever. I received the Pro Boost but, as I wished to switch to Anti, didn't pop it.
So, I do the Crossbones mission, the Choose Sides prompt appears, I choose Anti, and go to Cap's base, where I talk to Sharon Carter and get the Anti Boost, which I use. I notice that the Pro Boost is still in my inventory and, since it can't be destroyed or sold, I decided to use it. BIG MISTAKE. Now, I'm doing Anti missions and receiving Pro credit.
The only good thing about this is that I've been max influence since the first event, so that's not an issue. My issue is with the Seals of Conflict: Can I use them on the Cap vendor, or am I hosed?
edit: Apparently, seals are seals. Meanwhile, perhaps there's a way to fix this for future events, so noobies don't get caught up in the silliness.