In linter v3, the messages are flagged as removed and added. messages includes all the old "kept" messages plus new "added" messages. That means it is the responsibility of the linter-ui package to delete/add ui elements based on removed and added.
You should use a Map of message.key to message to store the messages in your cache and update the cache on each cycle based on the key. A Set of messages will not work.
See minimap-linter for an example of the changes.