When switching branches of an application using the source control feature in Studio. Records outside of the scope that are referencing records within the scope, will loss the reference to the scoped records. This is because the branch switch does a complete uninstall of the application (rip and replace) and then reinstalls the new branch. During the uninstall, the referenced record is deleted/uninstalled which causes a reference cleanup.
The record outside of the scope that is referencing the scoped record needs to be moved into the application scope.