I don't think you were meant to do that :P. The new mission journal makes it so all the missions are in a big long line (with the FE series branching of at Lt 6), you can't skip out any missions in the line, you have to play them in chronological order.
It used to be the case that you could 'pick and choose' your missions to play, but it's not so any more.
So that means I have to get past Frank Drake for Quinn to speak to me again? As I remember I'm not even suppose to meet Drake Until I reach the Romulan front.
The FE have been folded in with the storyline missions now. The devidians are now in the middile of the klingon arc the romulan FE with the romulan arc and the breen come after the the cardasian and because of the forced mission progression you now have to do the FE before you can continue with the rest of the missions
I think they have changed the episodes on Tribble a little bit too because of meeting Drake earlier. I think on Holodeck, you still meet Drake on that mission where you scan all the contraband and then inadvertently help him fake out the Romulans to beleive he betrayed Starfleet. On Tribble, I think Drake has been replaced by some lady who "fakes out" the Romulans with your help, since you already met Drake during the Devidians missions.
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It used to be the case that you could 'pick and choose' your missions to play, but it's not so any more.