If you really want to remove black hearts without having replay parts of the game. You can just cheat.
Steps:
1) Download RPAextract.exe
2) Extract Archive.rpa from the /game folder
3) Edit the file options.rpy with a file editor of your choice. I use Notepad++ but you can use anything that opens this type of file. Add in the line "config.console = True." Save and then close your file editor. Make sure you didn't use tab to edit the file. Only use the spacebar to add spaces.
4) Launch the game as per normal.
5) Press Shift+O to open the python console. Then type "logan_relation.love" to find the value. If you have one black heart, it should be -1. Simply change the value to 0 by typing. "logan_relation.love = 0." Do note that while this solves the black heart issue, it might / will break future interactions with Logan.
6) If you're not comfortable with all of this, then ignore everything I wrote and replay the game to avoid getting a black heart. Remember to save often.