When EDP determines external change in files being compared, it asks permission to update panels (according to "Ask" option). If I answer "No", previous versions did not ask the same question on further external updates till I do manual recompare. On the contrast, EDP v3.5.0.6-Beta asks every time. This may prevent working with EDP (and even exiting) if one of the compared files is being constantly updated by external process.
There's no differences in this behavior compared to 3.4.2. Also, you can always change the notifications setting right from the dialog, thus ending the notification cycle if necessary.