Putting the "B" ships in neutral rosters should not cause problems.
However, if any supermods have scripted in the existing "X" ships as part of the campaign's scripted layer, this may cause CTD's in campaign mode (because SH3 will seek the X ships and fail to find them). I don't think this is the case (GWX definitely does not script in MFM ships, and I doubt War Ace Campaign and the other supermods do). I think you should be fine.
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