When design system maintainers remove a variant from a component, there is a replacement variant that is intended for all current instances of the removed variant to map to. However, currently there isn’t a built-in way in Figma to prompt consumers in their files to make this global update. The missing variant remains as the instance, and there is only a button to “restore component” in the properties panel.
My suggestion is to have a “Missing variants” modal, similar to the “Missing fonts” modal, where consumers in their file are prompted to make a decision globally in that file to either keep the removed instance or replace/re-map them to another variant from that component set (or maybe even another component entirely).
Quickly mocked up how this could look, following design pattern in “Updates from Main file” modal when resolving conflicts in branches: