I didn't even know a mission like that would disappear.
To mitigate this issue in future playthroughs, I recommend that you do the following with any RPG or complex game with multi-tiered saving.
Create new saves, rather than saving over older saves. At least, at first. As you play through the game, get in the habit of rotating three saves. Save over the third-most-recent save, rather than the most recent. This allows you to go back two stages in order to resolve issues, and whether it's Skyrim, Fallout, DA:I or any other complex game, you will save yourself many hours of headaches from bugs or missed content by habitually saving this way.
In addition to rotating three saves, so that you always have recent checkpoints to go back to, you should also lock off a save every hour or two of gameplay. What I mean is that instead of saving over your third-most recent save, you create a new one. As you progress, your save list will eventually have the three rotated saves at the top, and a list of saves stretching back over your play experience every couple of hours (in your case this would be about 20 saves, which would be more than necessary, but this is a general guideline that works more easily with games that allow for 50-100 save files.)
In this scenario, you would go back to the most recent save in which recruiting Sera was still an option, losing only the time played since then, rather than all 40 hours.
As you can imagine, I arrived at this technique through having to restart many, many games (I'm looking at you, pre-patch Fallout: New Vegas) over the years. Now that I do this, I rarely lose more than an hour or two, and that's a worst-case-scenario. Usually, one of my rotating three saves is enough to do the trick, and I only lose 10-30 minutes (assuming I notice the issue early enough.) I also periodically backup important saves to Cloud or USB storage for the same reasons.
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