Code explorer doesn't remove a file's information if the file is deleted while open.

e.g. "utils.php" is open in phpED, I Ctrl-Del it from the file list, which closes the "utils.php" file contents window. Switching to Code Explorer reveals that the function/include contents from "utils.php" is still loaded in memory and there is no way to remove it from Code Explorer without shutting down the application.

This problem is addressed in phped 3.3.
Now you can see Code Explorer in different modes. See its local popup menu.