The only problem I have with ChocolateMouse's post is something that is implied, though not exactly stated - the idea that this sort of behavior is just to be expected from good mothers. IME, that is not the case.
I have been breeding rabbits for almost 30 years. When I started, I'd heard all the business about how you couldn't touch the babies or the mother would reject them; how you had to be so careful because even strange sounds or smells near the rabbitry could cause a doe to eat her young. I remember the first time I saw someone say that they kept their nest boxes in the house, and only took them out to the does once or twice a day. My reaction was, "You can't do that!" Well, I can tell you that you can do that; I've been doing it myself for - oh - 15 years or so. I have learned that does can be much more tolerant than I ever thought. Of the hundreds of does that I have worked with, I have had exactly one that deliberately savaged her litter, and maybe one or two that rejected theirs, in spite of what I consider enormous amounts of interference from me.
Some people will tell you that rabbits are friendly animals that like the company of their own kind. Some people will tell you that rabbits are solitary and will fight with any other rabbits. I think the truth lies somewhere between the two.
In their natural environment, the European wild rabbit that is our domestic rabbits' direct ancestor is often found in warrens or colonies, and some take this as indicating that they are social by nature. Actually, as adults, they are like other kinds of rabbits and are more solitary, it's just that human development and local geology crowd them together. In areas where conditions favoring rabbits are more widespread, the rabbits themselves spread out more.
Baby rabbits are instinctively gregarious - without the shared warmth of their siblings, they chill and die. As wild rabbits mature, the tendency to seek others to snuggle with is outgrown. But we humans like to snuggle our pets, so we prefer rabbits that are friendly and gregarious by nature. I think that by choosing rabbits that make good pets, we are selecting for rabbits that are naturally more tolerant in a lot of ways.
I sell a lot of rabbits for pets, and I've noticed that a certain amount of personality is inheritable. I have heard (and lived!) way too many horror stories of mean rabbits, so a docile personality is one of my criteria when choosing breeding animals. I know a lot of other rabbit breeders that do the same. I think this has resulted in a much more laid-back animal, one that will tolerate a lot more interference from us and reacts more favorably to other rabbits, too.
For example, I handle my babies as soon as they are born, and I put babies into other does' nest boxes all the time. I have even put them in as a doe was nursing her litter, and not had a problem. I have never used vanilla or anything else on my does' noses or their babies. I have had babies from several litters together for several hours, put them back with their mothers, and had no problems at all. I watch for negative reactions, of course, because I have seen them in the past, but it's been a long time since I've seen anything even approaching what happened with the OP's rabbits.
I am very glad to say that this has not come at the sacrifice of what I consider good mothering behavior. I was told that you mustn't do anything that could upset the doe close to the time of kindling. Many times, I have taken does that are due to kindle, and put them and their nest boxes in a small cage in my hall closet. I have had lots of does that build a nest, pull fur, give birth to the babies in the box, and nurse them, just as if nothing unusual has happened. Oh, yes, I have first-time moms that make a mess of things, but most adjust to the way I do things with no problems at all.
What the OP's doe did was within the range of "normal" rabbit behavior, but whether it's the kind of behavior the OP wants to put up with is for the OP to decide. It's kind of like the doe that attacks you if you put your hand in her cage - territoriality is normal behavior, but if it's too much of a nuisance, you can choose to work with rabbits that don't exhibit it.