I'm not entirely sure what the issue here might be, but if you suspect it might be related to this mod, the first thing I'd try (And what I'd try even if you don't suspect that, honestly), is to remove all your mods (temporarily), create a fresh profile, and run a test raid to see if you can extract without mods. -If you can, add them back until you can no longer extract. If you can't.. Try replacing your AKI_Data folder with a fresh version, and if that doesn't work, try a full reinstall of AKI on a fresh copy of your live EFT installation (After applying the downgrader patch, of course).
Thanks for the quick reply! I finally fixed it by deleting the cert file and adding it back in with root from command prompt, I didn't realize it was a large general issue, thank you so much for responding so fast too!