I very much doubt it could be “purely” psychological, but it can absolutely be from a dip in his immune system due to him being without his brother. Rabbits form very, very tight friendships and can become severely depressed when separated. That lowers the body’s ability to fight off or keep in check f ex mites.
It’s not uncommon at all for a skin test to come back negative even when there is a mite-infestation. Revolution can be used empirically, ie when you suspect mites but can’t prove they are there. If the Revolution then helps, there were mites. Sometimes with heavy infestations you need to treat more than once, Medirabbit says Revolution should be used 3 times in a row with at least 8 days between treatments. This is in order to kill mites in all life-stages. It seems odd that your vet doesn’t want to treat him again, if Revolution had some effect to begin with. Could you find another vet?
Rabbit urine can come in a variety of colors, all normal and healthy. The color varies a lot with the time of year, temperature and diet, amount of water consumed etc. A bunny that is itching or has some other physical problem like pain can “forget” about his good litter-box habits. If you get this problem fixed, I think he’ll go back to peeing in the box again.