If you don't add/remove objects (so object ids won't change) and don't change requirements, everything should work fine. If you add new units, ai won't know how to use them. If you remove units which are prerequisites for other units, the ai won't be able to use that part of the tech tree.
EDIT: In case I was unclear, I meant adding/removing units/abilities/other objects in the object editor, not adding them to map.