They DEFINITELY can.
There are two types of custody, legal and physical. Although Susan has primary physical custody, Michael has joint legal custody meaning that the court would see whether he is willing/able to be there to exercise full legal custody on a temporary basis. If something very urgent comes up in the middle of the night, DCFS will take them into emergency physical and legal custody to get them medical attention/ out of harms way. They would then go to the court and file an explanation for why they had to take the kids without court permission, and either request to keep the kids completely or release them voluntarily to Susan.
DCFS wouldn't do that in this case, so they'd likely ask the court to allow them to keep the kids in their legal custody with a release to Michael. Unfortunately, interstate travel with an open DCFS case is extremely difficult so I'm having a hard time predicting what would occur.
The best bet for Michael's getting full legal custody of the kids is for the court to assign it to him on a temporary basis, without DCFS having to remove them without court permission. Unfortunately, that requires an open Abuse/Neglect case, which would complicate Bodhi's PNP Center trip because the court limits out-of-state trips while the case is going on. Additionally, he wouldn't be able to get physical custody of Jani during this time without Susan agreeing to it for the same reason.
EDIT: The court can arrange for Minnesota's DCFS to keep tabs on the kids/family. It's not ideal or usual, but this case might be the best candidate for some interstate collaboration. For example, the kids can be under Michael's legal care but in an inpatient program somewhere.
Family law is a hot mess.