InDesign is the best option for me to create epubs. It creates very clean code if used correctly. Not sure what AIPe's problem is with it. Maybe he/she could elaborate.
There is definitely a way to do the search/replace with GREP for this but I'm not even sure you need GREP since you've marked it so well. Just replace all instances of [blank line] with a nonbreaking space (and a hard return before or after to put it on it's own line if it isn't already). Use the special character drop-down to the right of the Change To field. All paragraphs that contain a nonbreaking space are valid in epub and show as a blank line. That would be the easiest way.
If you don't want to use nonbreaking spaces, another way would be to use a script that looks for a style and then changes the style for the paragraph after it based on your input in a dialog box. To use this, you would change all the blank line paragraphs to a "blank line" style. Then use the script to find all of that style and change the one after it to a new style that includes some extra space before.
The script is here. It costs $39. There's a free one out there that does the same thing but the site where I got it is giving a warning message about malware so I don't want recommend it right now.
Also,
www.indesignsecrets.com is a great source for using InDesign to make epubs. They have an epub forum and there are quite a few experts there who have helpful advice. One of the sites creators did a great InDesign to ePub video on Lynda.com. Her name is Anne-Marie Concepcion. She posts here occasionally.