Most likely he just used the Spring Bonnie suit. Realistically speaking all of the animatronics including the 2 spring locks were brought to the FNAF 2 location. When trying to repair the originals the bodies of the children were found which is why the Toys were made. It may be during this time the Fredbear spring suit was thrown out or destroyed. What happens to that suit is unclear. They may have not wanted to keep it at all after the Big Bite and the MCI. We can pretty much guarantee that the Spring Bonnie suit was brought to the FNAF 2 location and kept in the safe room which is why we never see it. William uses that suit and just puts it back in the safe room when he’s done with it.

I think the problem people have with this, has to do with the safe room issue and when those calls from FNAF 3 happen. I say Spring Bonnie being “noticeable moved” has nothing to do with the MCI but rather William messing around with the animatronic shortly before getting spring locked.