I am installing recessed lighting. I removed two flourescent lights. Each had their own boxes with wiring going to them. I want to plaster over those boxes and run the wiring directly to the boxes that come with the recessed lights. Question: Can I patch over or put drywall over the existing boxes that I do not want to use? I know that if wiring is going to them that they have to be accessible. But what if wiring is not going to them?

you can patch over the boxes as long as there is no wire in them.
but you are much better to remove the boxes and patch tha drywall.