this may be completely backwards… but i know when i was younger we had cats… and the one kept peeing on the bed.  my dad who’s a bit of a hothead got really mad and took the cat to the shelter "to get rid of her".  the folks there said… try putting aluminum foil on the bed and when she jumps up, the crinkle sound will scare her and she’ll stay off.  it worked.  she never peed on the bed (or hardly even went up there) again.  would that work for a rabbit?

Wow I am so sorry to hear about Thumper.  There are a couple of ways you can approach this.  Leave his run space as it is and try training him by preventing him from going up on the couch with say a plastic bag or "Snappy Trainers" or catching him in the act when he goes to raise his tail, say potty and scoot or move him to the litter box. What do you do now when you catch the little stinker in the act? If a corrective method does not work I would suggest limiting his space until he re-develops his good habits again.  It is possible that since he was gone he is trying to establish himself as "top bun" too with peeing on things that most heavily have your scent on them.  The couch and bed are the two prime spots for this.

Like Scarlet Rose mentioned – it sounds like he is doing some “marking” up there unfortunately I would recommend only allowing him on the couch when you are there to supervise, I know limiting his space is tough – but it doesn’t have to be forever, you can just try for maybe around 3-4 weeks to train him not to pee up there by budging him off the couch when when he goes to lift his tail to pee. This will help you re-establish YOUR dominance, and that way you can still have couch snuggle time, but he won’t be able to keep his habit of peeing on the couch. BTW – a good way to get rid of pee is to spray it with vinegar.