There's actually multiple boxes:
And Maya usually seemed to barricade certain hallways with them:
Sensei does tend to help Maya carry at least one box between every reset, but the rest she might do on her own.
Why Maya did this isn't clear, but in theory:
These boxes may be there to protect, and guide whoever to the roof. The one reset she was unprepared for:
(Pareidolia probably messed with her head like it's probably been doing to everyone since Sensei connected to it) This thing showed up on the roof during that reset:
So, since Maya was caught off guard, she may have not moved all of the boxes to where they needed to be, leaving the roof vulnerable to supernatural stuff that normally wouldn't get past the boxes. (Possibly even why Sensei blacked out and killed her when he's usually came to his senses on the roof)
Considering that New Maya probably has no idea what the boxes or resets even are, the next time they go to the roof, they may have no protection at all.
As for what's in the boxes, whatever is in control of things doesn't seem to want anyone to know (besides maybe Maya, if she actually knew what was in them). Ayane saw what was in them but at some point it was casually erased from her mind that they even exist: