Like I said earlier, create a time machine backup before changing anything. And keep in mind you are posting in a Logic forum, questions related to Garage Band might be ansered here: GarageBand - Apple Community
In my Apple Loops library I have dozens of greyed out samples that don't load despite the circle with download arrow in it. Are those leftover indexed but unavailable loops from Logic Pro? That's ok but I hate seeing them in there:
They are part of the Apple Loop Library and can be usually found here:
~/Library/Audio/Apple Loops/Apple/Session Player/
These are very likely leftovers of Logic, maybe you didn't download them as they are part of the 72 GB Logic library. Either download the files or try to delete them in the Loop Browser. But re-index your library in the Loop Browser in any case. Is there a Sound Library Manager in GB like in Logic?
2. There is a file folder on my external drive with LP related files in there. Can I dump these or do I need them if I'm going to use only GB?
I really don't know, why the folder is located on your external drive instead in your User folder. Create a backup before deleting them.