My boyfriend is on both misdemeanor and felony probation only the misdemeanor probation knows about the felony but the felony has no clue. What will happen now that he has a warrant for his arrest with the misdemeanor will the felony know he was arrested or has a warrant even if he is bonded out right away? Are they on the same system? When he was arrested on the felony one the misdemeanor didn't know so can the same thing happen again?.

They did not know "right away" but part of the probation process is to run NCIC reports and it will all show up,

In fact one of the most serious violatoins is actually not telling the PO about the other problems. Even if they may just get warnings about the new violation , the not telling the PO will get them in trouble faster.

But it will all get found out and be the worst for it