meldrix:

I think Michael is mostly heart broken over his father but determined to stop him and undo his crimes at all cost. Before the Bite of 87, when William either ran or was arrest, Michael would have been old enough to remember his Father before the Missing Children incidents and the deaths of his siblings.

Although dismayed, he would probably hold on to a small hope that William would come around eventually and be the good father from his childhood. People in horrible situations often lessen how bad their situation actually is when they feel there is something redeeming about the person. I also think William would also threaten and intimidate Michael into silence over the murders until his absence.

That being said, once William tricks and sacrifices Michael to the animatronics at the Sister Location (in my interpretation) Michael resolved that William is truly lost all humanity and discards any sympathy he might have still had for his father. Seeming as William no longer had any remorse for his actions or even the murder of his own son, Michael locked away any evidence of who his father once was in the FNAF 4 box in order to keep himself from reconsidering ending his father, leading Michael on a path to ending William and his crimes for good.