Just got off work, thanks for the reply.
The modpack in question has an... odd history. It was originally a pack made for and by a specific server, and very tweaked and optimized. The guys who maintained it were masters of their craft, but, long story short, the server eventually closed. The aforementioned friend of mine decided to make his own server with this pack, and did so (with the makers' blessing) by copying the mods, configs and etc. from his client installation to a server one, then removing the client-only stuff. It actually worked well, and he later made a new pack based on it, with a bunch of additional mods. Now we have too many mods, and need to cut back a few to save performance. But, as mentioned in OP, removing mods shuffles all the IDs for some reason.
Apologies for the history lesson, I just hope some insight can be gleaned from knowing how things got to this point. Anyway, to refine my original question; What kind of specific pack tweaks do you think could cause such a bizarre issue, and what could be done to resolve it?