You are entitled to points for your room and one other. The third room is a goner. You don't say the status of your points posting, so I'll assume none of them have posted yet.

On three separate folios, it is likely the only one of them (the one which you, yourself, actually occupied) will get credit automatically. In that case you need to file a missing stay credit with Hilton for a second room, explaining your request in the comments field at the end.

Caveat: I ran across the problem that the system gave me the requested credit after I submitted such a claim. HOWEVER, in a slightly lower amount. I called customer service: the rep explained that the system had deducted the tax rate from the base $$ rather than deducting the tax from the net total charges. She adjusted the points correctly while I waited about two minutes.
Pay attention to this possibility after the computer adjusts your total stay points.