How to manage resignation for dual assignment

Summary:

We are using multiple work relationship(primary/secondary) for same person a way to maintain multiple employment of the employees over different countries.

While the above setup has allowed us to manage everything on application based on relevant country with some personalization, we are stuck with the process of Resignation. when employee tries to submit resignation on primary profile, it throws an error "you cannot end primary profile while you have secondary profile or something on same lines"

For employees having multiple work relationship, what is the best way to manage resignation transaction keeping in mind,

1. We dont want employee to submit resignation twice.