@brandflake11
I tried doing my initial plan of mounting the drive in fstab, but it didn't work either. I think What I'm going to have to do is like you suggested, using softlinks but pointing to a /external/ folder inside the rom/system folder. I did some testing last night, where I had symlinked the folder and had a few roms inside. I also have a gamelist.xml file and a /media folder where all the videos for ALL the games exist. Using the subfolder, I can see all the roms that are "internal" and a separate entry called external, when clicked on opens up all the games that are on the external drive. When I un-mount the drive and reopen ES, the "internal" roms are still there but the "external" entry is gone. This works by configuring ES to have the setting Always Parse Gamelist to NO, that causes it to scan for the files at launch. If set to YES, it will list all the games whether they exist or not. The nice thing is that ES will scan the roms and find some games with the drive disconnected and will still load the appropriate media (I think it loads them from the gamelist.xml in this case, where it sorta soft-loads the xml but isn't restricted to it). The only problem I have now is that the games loaded in the external folder (when it exists) it doesn't load the media. I think this is because it's still going to try to load the gamelist.xml and the paths no longer match. I'll just need to rescrape. That's what I'm going to try to do tonight.

So yeah, using a symlink like this works:

ln -s /media/retropie/Passport/roms/amigacd32 /home/pi/RETROPIE/roms/amigacd32/external

You just have to live with having the external games be listed in a EXTERNAL folder in your browsing lists. When I tried to do it on the file-level, it still tried to load and display all the linked files in the gamelist.