@voljega That's the problem, I didn't copy those over. Any way to get them back without re-scraping everything?

@voljega I restarted with a fresh new install of Recalbox on my SD card. Then I put all of my roms and my scraper images onto the USB drive. Now MAME is working with the games again but isn't showing a bunch of duplicates like it used to. MAME is also showing the scraper info and images, but every other system isn't! I have spent so much time doing all of this stuff and scraping roms and every time a new update comes out something goes wrong.

I just had the chance to do the update and now I'm having a couple of random problems. A lot of the stuff I had scraped is not showing. I scraped everything on my Pi and now certain consoles aren't showing anything at all, not just random games like before. Some random Famicom games wouldn't load. Then I went to Mame and all the games I had been playing, Galaxian, Galaga, Galplus, now they won't work. I hadn't played around with it much so who knows what else is possibly messed up. Anyone else having problems or did my stuff just not update correctly?With the update just before this one, something weird happened. I use the micro sd just to install Recalbox, then I have a USB drive for consoles, and one for all the arcade roms. When I booted it up all three ways it re-downloaded and installed the update. When I started the Pi up today I did so with no usb drives so I could mess with the new theme settings and not have it take forever to reload between options and it downloaded and installed this update twice. When I reloaded with my two different usb drives it luckily didn't try to install again (which is the way it always worked before). Sorry this was so long winded, I just wanted to make sure and give as much info so I can get the right help.

I have an update to my problem. I use the internal SD card just to install Recalbox on, then a USB flash drive for console roms, and another for arcade roms. As far as I can tell, pairing the controllers doesn't pair it to the Pi itself, but rather pairs it to each devices settings. The problem is when I tried to just pair it with the other drive, it didn't want to pair. When I hooked it up with a USB cable for a bit, then unplugged it, it let me pair it. However, when I tried that same method later, it wouldn't work again. Does anyone have any ideas?

Thank you!

On my Pi 3 after the 4.1 update downloaded the first time I tried pairing my DS4, it worked. Then when I plugged in the USB drive and rebooted it, my DS4 wouldn't pair. I ran into other problems so I did a fresh install, after which the DS4 still won't pair.

What new bios files, if any, will we need for the 4.1 update additions?

@substring I actually just figured out the problem and came back to update. All of my files are on an external device. I checked every other system and things worked fine. The problem was with the syscard3 bios, I just downloaded a new one and it fixed it. I don't know why the other one quit working when it was fine before.

I upgraded to the Pi 3 and now my PC E CD games won't work. I transferred all of the bios files and checked the .bin and .cue to make sure they were lower case. Everything was fine until I switched to the Pi 3. I checked all of my other emulators and they are fine, so I don't know what to do now.

Thanks for the info, I'll try to find the best / easiest way for me to move the roms and themes and stuff over.