Disk Full Message When Scraping

[SumCanadianGuy]

I have RetroPie running on my Zero on a 64gb card just to make sure I have enough room for everything. I have ~23GB of ROMS and I am trying to mass scrape them. There are ~7,000 ROMS and after ~1,000 it says the disk might be full. I don't think there is any possible way that metadata for 1/7th of the collection has taken up all the remaining free space. The file system is expanded so I am kinda lost on this one. If I tell it to cancel when the error pops up and I run it again it will scrape a few more (very few, last time it was 16) then give the same error. Not that it should make a difference but I will mention that I am running the scraper with the card in my RasPi 2 because I don't have a hub at the moment.
Another note, I had RetroPie installed from the Zero image and I mistakenly updated it while it was in my Pi 2 and Emulationstation wouldn't boot when I put the card back in my Zero, so I used the RetroPie script to uninstall and re-install RetroPie and update it via ssh with the card in my zero. Did it leave behind some garbage that is filling the card? I'd really rather not wipe the card and fresh install again as it takes an age to transfer 23 gigs over the network to the pi.