As an experiment I added a note to a verse plus I highlighted one word in the same verse. Then I selected the verse and right-clicked on "remove annotations." Not only did the "note" disappear, BUT so did the high-lighting.
Since Logos 4's release in Nov of 2009 -- "annotation" has NOT mean "highlighting." If you see lots of "confusion" now by beta testers wait until that change makes it to the "prime time." of a Stable release. Our Forum "stars" already (expertly) hand out detailed "fixes" to confused "newbies." The ["a 'annotation'" is 'really' a "highlight"] change is going to confuse/frustrate a lot of people who will then be posting looking for help.
ie. even those on beta are confused: http://community.logos.com/forums/t/39641.aspx
Therefore, if this "new" way of [looking at/naming] highlight-annotations is to be the ongoing pattern, a MAJOR re-explaining of
"terms/definitions" will need to be done before this Beta (whatever its #
becomes) "automatically" replaces the present stable versions.
EDIT [ It appears I should have posted this comment here: http://community.logos.com/forums/t/39610.aspx ]