I'm working on another conlang for my world and its evolution, and one of the defining qualities of its handling for transitive verbs in sentences is using nominative-accusative alignment, but switching sentence structure from SVO to VOS when doing so. what im wondering is if it could potentially make sense that a language that does this would switch from nominative-accusative to ergative-absolutive (on the idea of languages preferring context initial grammar rules) without changing the sentence structure again, and if so, are there any natural languages which have ever done anything similar?
VOS languages are rare, but frequent enough for some analysis. Combining basic word order and alignment in the WALS sample we find two languages with VOS and absolutive/ergative alignment, and only one language with VOS and nominative/accusative alignment. This is not enough data to draw statistical conclusions, but probably enough to justify a switch of alignment in your conlang as naturalistic.