Ok, thanks for the feedback people, this has been changed to reflect requests and ideas I have leeched from the forums.
PLEASE CLOSE LOGOS4 BEFORE YOU TWEAK
Changes:
- 5 levels of notes/markup databases backup/restore
- Restore gives you a choice of restoring markup and/or notes.
- Visual Filter - Change Pallette
- Remove All markup/highlighting from a book (not notes) with one click
I realise Logos has removed the reorganization of Markup Pallettes for the moment, so I guess this is the only way for the moment (this part was written in v2 but not released.) Its not pretty but it works, as I know L4 will be bringing it back soon(ish) I will not be updating this particular feature.

Again this is meant as a temporary measure until Logos fixes things..
Download Here
2577.NoteTweaker_v3.1.zip
PLEASE READ THE README