My rabbit doesn’t really like to be flipped either, but I flip him and put him between my legs on the couch so I can cut out any icky goobers around his butt. I place a comb underneath the offending hair and keep the comb between the rabbit’s skin and scissors at all times. Sometimes I use warm water and a paper towel to try to loosen it if it’s too close to his skin to be cut out, and I might split it up over a couple days. When I was ill and un able to check him and he was molting really bad, he got pretty nasty–but a couple of sessions (spread out over two days) really helped. I had my husband hold him sometimes when he wanted to wiggle, especially his head, stroking his cheeks and reassuring him.
I’ve found that making sure the rest of him is deshedded– like, his back and such, the places he doesn’t mind me touching–seems to help him focus more on the areas he doesn’t like me touching during self-grooming, so maybe increase general brushing, especially during a molt, only flipping him over occasionally since he hates it so much. Also, now that he’s bonded with two other rabbits, they help him stay a lot cleaner (my Scully bun, especially, loves to groom.)
Sometimes it seems like all rabbit problems can be solved by buying more rabbits :p how convenient.