@billydv - This due to you shouldn’t do that, AFUDOS w/ GAN made for BIOS type decade+ old, and 1-2 BIOS series types older than Z87/Z97 BIOS. The actual cause of what you mention is due to NVRAM not being programmed back in properly.
Do this, if you must continue to use AFU >> AFUDOS.exe biosname.bin /P /B /N /GAN
The proper way to do this instead of using AFU, would be use FPT but only if you are modifying the BIOS would any of this be required. Dump the BIOS region from target board, modify that if then flash back to that same board only using FPT.
If you are simply updating the BIOS, without modifying it, then use UZ Flash and stock BIOS as it is from Asus, nothing special needed except to rename it to USB Flashback name and put on FAT32 USB and then enter EZ Flash from within BIOS.