Maybe you can add an option for "Save links to file" like this:
Where we could choose save links with separator added in the end of link or without it.
You could keep marked as default without separator and a box for we mark when want the separator in the end of old link.
Or you could just add a check box in the popup wiindow where we choose the folder/name to save the txt file, with the option "Save links with separator - | ".
And when this option is marked, the links are saved with it in the end.
This method to replace links with separator would be used when we had posted links without file name in the url.
And it would be very useful for we create the txt file with the new links, to replace the links wtih hash by links with file name.
But, please, don't remove the "empty lines". Lets the "Save links to file" working the way it is.
Because with the empty lines is more easy to view the hash of old links when we need to check with the hash of the new link.
With the empty line between the links is more easy to view if we pasted the new link in the correct position of the old link.