What if you add these steps between the #1 and #2 you have listed:
Pull first line from file (without delete)
Check to see if that line was blank or not.
Quick question though - just want to verify that the file exists but is blank, right? Because if it is completely gone there is actually a macro you can use to check and see if the file exists.
*EDIT* Sorry, somehow I missed the second half of your post where you explain that you don't want to make a separate branch for each of the files to check if it is empty. Your explanation makes me more curious though, are you sure the files were blank? Because in my experience if you delete all lines with Zenno (as it sounds like you are doing at some point) it will not simply leave a blank file but completely deletes the file.