Either they should be flagged or there should be a way to get them again if you do ever get rid of them. Like running the facility 4028 mission again should be able to reward you with the 3 doffs that it did the first time, provided you didn't have them in your roster.
If you're speed selling without checking, it's your problem. It's why I look twice when selling Energy Weapons doffs since I have a cannon stash.
What does it have to do with speed selling? It's just that there is a group of ~18-20 doffs which, when compared to the tens of thousands of other doffs in the game, you can never replace if you ever were to sell them and there is no message that those doffs are one-of-a-kind.
Who cares if you dump a doff from a random defection doff, one with a special active ability or even Industrialist Krinda? Even if it's a lot of work you can replace those. You can't replace the ones from the Facility episode and 7/7 colonial, other than deleting and rerolling the character.