I find it depends on the rabbit (today I examined Leila’s ears because I’m worried she’s scartching to much and although she nipped and struggled at points she forgave me after I set her free and soon after she felt comfortable and came back near me). Similar thing happened to me– we took Pudge to the vet and the vet turned out not a rabbit savvy one and pushed poor Pudge down on the metal counter, also his assistant pushed him down too! We brought him for nail clipping–he clipped too far and it bled a small bit. When we got home Pudge was NOT a happy bunny! I let him run around my room and he sat behind my dresser refusing to make contact with me at all costs.
Anyways he’ll come around. Best way I make up with Pudge is leave him alone,I let him have his space and when he wants to, he’ll take the BIG step and run past me/come near me. I figure that’s a sign of giving in… like, “okay I’m doing what I want, just don’t make me mad again or I’ll hold another grudge…” lol.