So, I've merged a couple of weapon mods together using Fo3Edit. It worked perfectly.

However, now the assimilator .esp lists all of the merged weapon mods as it's master.

Is there a way to merge mods using Fo3Edit without it listing all the assimilated mods as it's master?

Or, if there isn't, would it be harmful to just remove the masters?

I'd have to see to help, but it might be better to merge the records in your .esp (upward) into one of its masters than (downward) into a dependent .esp.