I don’t know if I’m understanding what you are saying - there are no rafters in the roof at all? That would be pretty unusual.
Usually the foam boards are held in place with insulation straps stapled to the rafters on each side.
It’s possible your roof was constructed of “foam core sandwich panels” (you can google them) and then the rubber roof was glued in one piece to the top of those panels.
If that’s the case, you would have to replace the damaged panels by duplicating the original panels, and glue a whole new one piece rubber membrane on top. This is going to be a big job.