all that really contradicted the canon in cotm was Drac. he was resurrected twice in a span of 10 years, and killed by a bunch of unrelated hunters.
were they to retcon drac and put carmilla in his place, there'd be no real contradictions. the game would lose the last real connection to the series though, seeing as there's no castlevania (the game happens in carmilla's austrian castle), no vampire killer (instead we get a generic hunter whip) and no belmonts (but a bunch of newcomers).