Damn, Yoake's look of anguish as Arata talks about his hope for a future with Hishiro is powerful, coming from someone that's almost always a smug kitsune-eye guy.
Honestly speaking, even if the experiment does totally wipe their memories of each other, leaving just a vague suggestion... I do kind of feel like the two support members could set them back up together anyway, try and send them to work at the same company, etc. The subjects only have their own memories wiped if they fail, not if they succeed, so they should still have a vaguely each-other shaped hole left in their life waiting to be filled. (The way it's been talked about up until this point, you'll still have memories of 'some person' being there, just not specifics. Like a childhood crush whose name and face you've forgotten. You remember they were there, but you can't remember who they were.)
Ignoring how illogical the memory wipe mechanics are to begin with, It's also not a rule thing. There's no reason the handlers can't explain what happened, that due to a quirk in the system their memories of each other were affected, and set them up to get back together. They could even have recordings, potentially.
That being said, I doubt the author has thought it through to this extent and will probably just go for a memory wipe bittersweet ending without really acknowledging the relatively simple ways of at least trying to deal with it.