Is this an oversight or did I do something wrong?

Okay, I recently reformatted my computer. I have a relatively recent backup of the CoH folder I keep on my external HDD so I copied that over. Not a problem.

I went into the game and looked over my arc (Shadows In Your Mind) and saw that there was something that needed changing so I republished it. I then noticed that the custom group I made only had named characters within the arc still in it. All the Lt's and Minions I made had disappeared.

Like I say I reformatted my drive so the information for these minions isn't there, so by republishing it did I effectively wipe out half of my own group? If so is there any way to retrieve them as I worked a long time on them but also can't quite remember the powers of all of them.

If this is a weird oversight in the system is there anything I can do other than just manually recreating the group from the top of my head?

I haven't seen it documented, but in my experience republishing an arc gets the critters from the .critter files on your hard disk. If you edit critters in a published arc, you'll see that the files are changed on your hard disk.

So, yes, what you describe makes complete sense based on what I've seen: if the .critter files are lost and you republish an arc, the republished story will lack the missing critters.