I hold a non EU B permit for a Phd, and my wife is here on a family reunion permit. She needs to return to our native country for a while somewhat urgently, and she is getting a return visa done for it, since her permit is currently being processed for renewal, and based on what the OCP in Geneva is saying, it is likely to take a while.
Due to reasons related to my work contract I need to change cantons during the time she will be away on the return visa.

So my question is, If I change cantons, will her return visa be valid to re-enter Switzerland so she can register at the new canton when she arrives?

Any info is greatly appreciated.

Yes, she'll be fine. When you change address you will change it for both if you.