Deleting the associated .mbp file to remove highlights and notes for a book seems to have worked on the K2 for some people, from what I have read, so perhaps it will work on the K3 as well, but as I don't use the highlight feature, I obviously have no experience with adding or deleting highlights or notes. Try it out - copy the file to your computer first, just in case, then delete it from the Kindle and see if the result is what you are looking for.
Here is some info on clipping limits that may help you:
http://www.kinworm.com/2010/09/highl...on-kindle.html
http://realtech.burningbird.net/web/...lipping-limits (this is for the K2)
The second link appears to indicate that there may be no easy way to accomplish what you want - hopefully someone here who has run into the same clipping/highlight limit problem can help you.
Holly