The mere fact that two rabbits are related does not by itself create genetic issues. Line breeding is done all the time, often with closer relatives than this, without any noticeable problems. If you took two animals with "perfect" genes and bred them together, their offspring would also be "perfect," even if the parents were brother and sister. The thing is, the smaller your original gene pool is, the more likely that any particular genes (good or bad) are shared by the parents, and thus will get "doubled" up in the offspring. (This is how strains of laboratory animals get created - by breeding close relatives together for enough generations, they wind up with a line of rats, mice or whatever that are so similar genetically, they are basically clones. That way, an experiment can be run, and they can be reasonably sure that any difference seen in the lab animals is the result of whatever was being tested for, rather than some random gene that just happened to be different between the two groups of test subjects)
If, by some random chance, there is something "wrong" in the genes of your two does, that also got passed by the one doe to her son, then it is possible that the fetuses died as a result of a genetic disorder. But it is just as likely that you caused physical trauma to the fetuses when you were palpating, and they died as a result of that. Or, it's also possible that you are mistaking what you are feeling, and the doe is still carrying the same number of fetuses as she was a week ago.