Welcome to Tom's Forum!
If the problem didn't occur prior to you removing the "NTLDR" file then a BIOS flash certainly isn't going to 'fix' anything. Frankly, I'm surprised you're booting properly with the file missing.
Yes, EZ Flash 2 is the 'safest' way to flash your BIOS.
If it were 'me' I would probably backup all of my data, reformat, and reinstall a Clean copy of your OS, and install all of the latest drivers per ASUS for a starting point.