In LiClipse you're expected to edit only the theme. All colors -- including annotations -- are then updated to match the theme (they're applied when you change the theme and when it's restarted).
So, to fix your issue, you should edit the theme itself.
Go to the preferences > general > appearance > color theme
and to change the theme click on edit theme
.
Not sure which of the annotation related colors you want to edit without a better description, but the most common is for occurrences, which is given by occurrenceIndication
.
As a note, another solution could be choosing Don't reapply settings on restart
, so it wouldn't apply the theme on restart, but things may become unsynchronized then and changing the theme would override your manual changes too.