The easiest units to replace are the two assassins (they have 2 unit IDs each; set them to their alternates, and use the good ones), Alma 13 (used in one cutscene, easily replaceable with battle Alma), Simon, and Balmafuma, IIRC. You can even use Dead Malak, in a pinch (though I'd suggest setting something aside to be always:dead and equipped to him for the relevant battle)
Go through the ENTD, and make sure to fix all the cutscene errors that would occur as a result, and you should be fine
Go through the ENTD, and make sure to fix all the cutscene errors that would occur as a result, and you should be fine