Overwriting canon is fine, actually. TOS never had an issue with it, and PIC S1E10 gave Data a much better send-off by breaking canon from Nemesis and other Soong episodes. Gene Roddenberry’s assistant officially decanonized TAS, but better writers still acknowledge it.

The idea of “canon” in regard to fictional worlds is dubious anyway, especially ones developed across multiple writers and generations. I’m fine with stuffing Pike’s comment about women on the bridge into the dustbin of history, and not stressing about what decade the Eugenics Wars happened, and assuming PIC S3 doesn’t exist.