So I upgraded to the paid version but the highlighting in the free version is still in the paid version. How do i get rid of it?

Not sure, since I've never used the trial version, but what happens if you uninstall it, reboot your machine and install the paid version instead? I seem to remember that someone solved the same issue that way earlier.

Another possibility could be to go to the main menu Tools > Highlighter Colors ..., and then choose the Default as shown in the screen-shot attached.

Frank