I have a bit of a different take on desensitizing rabbits and other prey animals, based on experience training our llama (under the tutelage of an expert, whose techniques come from horse training) and working with our own rabbit, Amelia. The basic idea is not to completely shield your rabbit from normal everyday experiences that scare him/her. Rather, it is to repeatedly, gradually, humanely expose the bunny to experiences that frighten him/her, while the bunny is in a safe place.
NOTE: Don't over vocalize with "It's OK, it's OK," because the rabbit will pick up on any tension in your voice. If possible, use your calm body language rather than your words to soothe the rabbit. Of course, if you are teaching a trick (like standing up for pellets), use your training word consistently.
Here are several examples:
Example 1: Rabbit is afraid of being transported. Put the carrier in the room, with a litterbox, hay, and some pellet treats inside. Let rabbit explore, go inside, have door closed, have door opened. Relax. Progress to picking up the carrier while animal is inside. Return carrier to room and open. Eventually, progress to putting carrier in car, returning. Driving around the block, returning. Driving to the vet (no exam), and returning. You get the idea.
In other words, break the scary experience into very small steps that help animal realize each step is safe and, therefore, the "big step" is also safe.
(In horse/llama halter training, we start by having the halter hang around the animal's living area until it's no big deal. Then we move the halter close to the animal's head, and back away. Then close to the nose and away. This progresses until the halter goes on the face without any scared response. We do similar activities with noisy objects such as empty soda cans in a bag, things touching their legs, and many more activities.)
Example 2: Scary sounds. Amelia was terrified of even the tiniest sounds, such as a nose sniff or a door opening. She would literally flip out, as Mary's rabbit has done. The solution involved two people and the rabbit. Person #1 sits with the rabbit in an enclosed area, calmly petting and not paying attention to Person #2. Person #2 performs the "scary" act while Person #1 remains calm and makes it clear to the rabbit using body language and petting that this is NO BIG DEAL. Over time and repeated exposure in small doses, bunny learns the situation is not scary any more. The key is for Person #1 NOT to react, stay calm, and either distract or soothe the bunny while Person #2 takes care of making the noise.
Example 3: Picking up the rabbit. Start in a small, enclosed area such as an ex-pen or a bathroom. Be sure the rabbit is comfortable with you sitting calmly in the area and can accept petting or touching before you start this. Lift the rabbit just an inch or so from the ground (in a safe, fully supported position) and put him/her down again WHEN THE RABBIT IS CALM; let the rabbit relax fully before trying again. Be calm and matter of fact. Do not talk to the rabbit other than to use a training word such as "pick up." Repeat the process, gradually lifting a bit higher each time. Do this in several sessions over a period of time.
The KEY: Rather than avoiding the scary issues altogether (unless they truly are unsafe), address them head-on, but in a gradual way that helps the rabbit understand he/she is safe. Be patient. Take your time. Break everything into small steps. Stay calm. Transmit that calm to your rabbit. Keep your voice quiet or very low.
Over time, your rabbit will learn he/she is safe, and these "scary" activities are not to be feared. Eventually, vacuum cleaners, doors slamming; human sneezes, coughs, sniffles; cleaning in the area; being picked up; etc. will be much less scary (if scary at all). Of course, a NEW and slightly different situation might cause alarm, but then you just start back at square 1 with THAT issue and work it piece by piece.
I hope this is helpful. These desensitization techniques have worked well for us and for many prey animals we've worked with.