I've noticed that some behaviors will disappear from them panel, and others will show the red red exclamation mark if code is modified.
I've also learned to be very careful with UE 3 and 4 when using the DW button to create or edit the email content. This is such an useful feature, especially when posting dynamic data into the email body, but it can be finicky.
First of all, say you're on the page that you're applying UE and that page has a recordset or more. When you click the DW button to edit, the wizard will go away and the editing page will display. This page will also show the record sets but with the exclamation mark. It's tempting to double click those and "fix" them, but doing so will mess things up.
Second, when you're finished editing, you must press control-S which will make the temp page go away and the wizard reappear. If you attempt to close that page, it will ask if you want to save it, and you say yes. BUT this does not bring up the wizard again. The waue file is a temp file only, and should not remain in the file structure. It sounds like that's what happened.
When you do it the correct way - control - s, it actually copies the code to the original file, or the helper file if you've selected to have one.