I had this issue, and it's at an awkward part of the game. The only way I can accrue enough points to get to the mission after "Sleepers" without replaying a mission is to run a LOT of Doff missions (1,600 points away from the next level last night).
Yeah, had it restart on me as well. This was an old bug I encountered when the game first came out. Had gotten into the habit of hailing Starfleet before I exited the map to complete my missions. Thought they had fixed it, so I broke myself of that habit. Looks like I should keep doing it that way for safety's sake.