Meshmixer is a challenge to slice a design. I had similar problems to yours. If I remember correctly I would do a slice and then save and try to do as few slices as possible to get a printable section. I sliced on very set lines so I could always start with the complete design and just slice out one section at a time. I was disappointed in Meshmixer but didn't want to go up the learning curve on another tool.
Carl
