I've found a workaround after @victoria's comment on this issue
Before protecting your apps and syncing all your relevant Retool instances, make sure the app's resources exists in all Retool instances.
Once the resource resource-abc exists in all Retool instances (dev, staging, and prd, for example) then the github sync can be done successfully and Retool will be able to migrate your apps to the instance resources (even if the UUID is different).
The error I did was to git sync my apps, and after that, create the resources... Resources should exists before git syncing (or even importing) the app. Retool's "app migration" will then take care of the rest. Resources in all instances should have the same name of course.
Would be nice to point this out in the doc...