This is exactly what I was looking for - Sorry for the vague description!

Thanks for the help.

Your use of “clear” is ambiguous. That might mean “clear the marks” as in remove the highlights or circles (like Alan interpreted). Or it might mean “delete the lines that had marked text” (which is how I’m interpreting it).

In order to be able to do things with the lines of marked text, when you use the Mark dialog, you need to remember to checkmark ☑ Bookmark line as well.

Then you can do the search to add the marks (highlights) and bookmarks (circles). Then use the Search > Bookmark > … commands (*) to delete the bookmarked or unbookmarked lines. (*: or right-click on the bookmark margin to access the same menu of commands)

If I have a file with the words one to five on separate lines, and want to delete only the lines that contain the e character, I could:

1. Mark and Bookmark those lines
   
2. Use the Bookmark menu to Remove the Bookmarked Lines
   
3. End up with only the non-matching lines:
   

Using the Remove Non-Bookmarked Lines would do the opposite, deleting two and four and leaving the other three words.

Hopefully one of us interpreted you correctly.

You’re comments are very vague, but try this:

When you are clearing the bookmarks (i.e., pressing the button to clear), make sure the Bookmark Lines checkbox is checkmarked.