There are no special steps required for updating from BIOS version later than 0099 to a more current BIOS version. You needed to confirm that Management Engine version 8.x was installed in earlier steps before updating to version 0099.
It appears you skipped these steps:
If the computer’s current BIOS version is 0048:
1.Check if the Intel Management Engine (Intel ME) Firmware is version 7 or 8.
a)Press F2 during boot to enter BIOS Setup.
b)Go to the Main > System Identification Information screen
c)The Intel ME version is listed here.
d)Press F10 to exit BIOS Setup.
2.If the Intel ME version is 7.x, use the BE0048.BIO file to do a BIOS Recovery and then check the Intel ME Firmware version again to confirm that version 8.x has been installed.
3.Then update to version 0099 before updating to any later BIOS version, using one of these methods:
Express BIOS Update
F7 BIOS Flash Update
iFlash Update
Once a board has been converted to 0099 or later, it will no longer be possible to downgrade the BIOS to version 0048 or earlier. Attempting a BIOS downgrade to a previous version may fail –the board BIOS will remain at its current version.