If you have access to the inside of your computer then locate the BIOS reset pins on the mother board. That will reset the BIOS to the default settings. Your newly loaded BIOS should boot then. If you don't have access then place the old BIOS file on a bootable CD/DVD. Then place the CD/DVD in the drive reboot your computer Back in the day of 3.5 drives this could take some time to recover. The longest time it took me was 30 minutes. So give it some time. I always set my old BIOS to default be for I install new BIOS.
If your system boots up go in to BIOS and make any changes that need to be made. If you're not running a custom settings you can boot directly into windows. By the way is this system a lab top or desktop? As lab tops can be a real pain.
lucky me to have an antique Toshiba Satellite 2800 notebook with a floppy drive that still boots up, the CD/DVD is not able to use burned CDR media, drive is way too old for that. If the hard disk ever dies, I can still resurrect it with compact flash, i found on ebay a notebook EIDE adapter that holds 2 CF cards
the machine being repaired is the Satellite Pro A210-MS5 notebook which has more RAM etc and is SATA so its more repairable
so i can make a DOS disk and use that to master a boot disk with any version of MS-DOS desired
I have the original BIOS on a USB stick at the moment awaiting deployment
I also found a DOS flash tool for the BIOS but not sure if I need that, lots of tools depending on the BIOS de jour
so why not try to flash the upgraded BIOS?
You could try the new BIOS again. But you are having problems with it. I would try the old BIOS unless the new one has fix that you need. First go to the site for your lab top and read the instruction for updating your BIOS. Being that you have a 3.5. create a bootable floppy, then place the old BIOS on the drive, just the file. Then put your floppy in the drive and boot up your system. Give it some time, say up to a half hour, if nothing happens, put the DOS flash tool on the disk with your BIOS file (old). try and boot up MS DOS, If that works, put your floppy with the flash tool and BIOS file. It's been along time since I use MS DOS type in A:\ (this should be your 3.5 drive) hit return. then type in A:\ dir you should see what is on the floppy type in the name of your flash tool it would look something like A:\ flash tool.exe hit return. Once the program is running you'll need to tell it where the BIOS file is. Once it finds it hit return, it might ask you to save the BIOS, in your case no. Then it will load the BIOS file that you put on the floppy. Let it do its thing once done. Remove the floppy and boot into you BIOS make any changes then reboot into Windows.