We had a similar situation this evening.
I was meant to join a friend and accidentally ended up in the briefing room with a couple of random guys and was saying oops, I'm off to join my friend, but they got me to bring my mate in to do some missions with them.
They'd only done the prologue mission, while we'd already done the first few after that.
We didn't want to spoil anything for them on the mission or two that we'd already done and just tried to play it like it was all new to us.
I went in as engineer for the first time, whereas previously, I'd been flitting between helm and tactical, while my friend stayed as captain.
It was great fun and we all had a proper laugh. We now have another couple of good lads to play with too.
I guess it depends on who you're with tbh and I wouldn't worry too much. If you are that concerned, then just make it clear to your mates before you start the mission and hope that they act accordingly.