I can't imagine any mod removing that on purpose. Might be an install routine that didn't merge properly.
Normally I would say just add that in yourself (after backing up DDE, DDF, KDF, etc) because that entry is primarily for exposing tables to VI and for flowing UDFs through _Upd objects, not for regular programming. You would add not just AR_Customer_bus but whatever else you see on your own system for the same version.
Alternatively reinstalling A/R would do the same thing. Also to answer your question, I can't see how adding this hurts the mods in place unless they are doing something non-standard.
My official answer is ask the mod developers about adding this entry. They may need their own _Bus or _Upd classes added for AR_Customer on top of what Sage adds.
Therefore in the end, the best non-hack approach here maybe reinstall A/R then reinstall the mods.
If this is clear as mud, call me or send chat.