What do you have for leaves on those clones? And have they rooted yet?
Buds can be a place for rot to start, but if the bud leaves are all that you've got for photosynthesis, you don't have any choice but to leave them on, and the bud along with it.
Generally when you are revegging, removing as much bud mass as possible while leaving leaves is desirable- a high ratio of leaf to calyx is what you want, and if there are any seeds, get them OUTTA there.