So far as I know, the css trick in the manual:
Code:
[class="sigil_index_marker"] { color:#335500; }
only works to highlight words that were
manually (and individually) marked using Tools->Index->Mark For Index.
Entries that were indexed automatically using the Index Editor do not get wrapped in their own individual anchor tags. So the css trick will not highlight those words.
You should be able to easily remove entries from the Index Editor that you no longer want by right-clicking on the entry (in the Index Editor), choosing 'Delete', Save, and then regenerating your index. Using the Index Editor will not affect any of the words you've manually marked for indexing. You can still find those by using the css trick you mentioned (or by using F&R in regex mode in Code View and searching for "sigil_index_id_\d+"). Once you find them, you can remove the index anchor tags from around them and then once again, regenerate your index.