Is the separation of two friends due to one of them being preoccupied with preparing a master's thesis, while affection and prayers remain between them, considered a punishment, or does it fall under the nature of separation as happened to the Companions after Medina?

A Muslim is the brother of a Muslim; he neither wrongs him nor abandons him. And two people do not love each other, only to be separated, except by a sin committed by one of them. So if your companion changes towards you, know that this is due to a sin you have committed. Therefore, repent to Allah from every sin so that his affection for you may be restored. This separation does not apply to separation due to travel or death, provided that love remains.