The adoption of R4 in the Healthcare API has been much higher than previous versions. It is fair to say that R4 to R5 will be the first significant upgrade we will have to handle, as the STU3 to R4 transition was much earlier in our product lifecycle.
Mechanically, the Healthcare API supports (and will continue to support) all versions separately. The FHIR version is chosen when creating a store and does not change later. You can still create DSTU2 stores today, if that's the data you need to handle. So as a baseline, customers can always decide for themselves when and how to migrate by creating new stores.
There are various things we could do to make the upgrade easier - mapping pipelines, on-the-fly facades, etc. We are still evaluating what would best meet our customers' needs. There are some inter-version mappings developed by HL7 (
https://build.fhir.org/ig/HL7/fhir-extensions/conversion-registry.html), but one-size-fits-all transformation is not a realistic goal so we'd have to allow for customization.
This is still a developing area for us, and for the FHIR community in general.