I’m not sure they will do that. I guess Fairphone has access to their signature keys, but I don’t know the details of wether and how they can flash a modified (but signed) software to recover a Phone the factory reset protection has been triggerd on. You’ll need to contactsupport to get more information on their policy and technical abilities with regards to that.
But while you’re at it you can also ask them to compare the IMEI of the Phone against their database of stolen phones that’s mentioned in the post linked below. Just to be sure.