Based on this lovely scene that my friend Katerina took the time to write : Confrontation

 Possession is surely something an experienced black magic user like Phobos is very familiar with. It's a useful trick against enemies as they would most likely refrain from attacking a loved one. Elyon is completely helpless while facing her son.

 However there is a catch: for the possession to truly work both the possessor and the host must share an emotion, something that connects them, In this case both Dante and Phobos share the pain and hardship of being born a male Escanor. 

 Also, even when the one possessing is in full control he cannot do it without permission nor can he replace the host's soul, only share the body. 

 I imagined that Dante made many other visits to his uncle at his dungeon and ended up with a venerable mind full of doubts to which Phobos promptly took advantage of.