What does it mean if my boyfriend is in cusody and their is now a flag for immigation can he lose his green card

If "he has felonys", it may be that one or more of those felonies are a basis for deportation from the US, especially if those felonies involved violence, moral turpitude or domestic violence.

Persons who are not US citizens are subject to deportation for a variety of reasons.

Since your post lacks relevant information, the most anyone here can offer you is that your boyfriend should promptly review his specific facts with his attorney. Sometimes, the government works very quickly in deportation cases.