In the 'Logical Files' tab of ECL Watch, if you open a file (by clicking on the name in the list) then that file is checked (i.e. the checkbox is ticked) in the list tab. If you then go back to the list and change the filter then the check is remembered. So if you check a file and click on Delete then you're asked if you want to delete both files. I appreciate people should read all confirmation dialogs carefully but, well, they don't, and it would be very easy to accidentally delete a file that shouldn't be.
Was this a deliberate decision? I can see why it behaves as it does, it could be useful to remember checked files when changing the filter, but I can't help feeling the additional utility isn't worth the risk.