I haven't played the Medmod for quite some time, but I believe that the "2" refers to the Byzantines that you can play in the late period.
Wes probably wanted to create a new faction slot for them to escape all the hardcoded stuff originally associated with the Byz (such
as the influence bonus). The Byz in late are supposed to be weak, after all.
So yes, It would create problems to delete the "2".
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