Flashing a motherboard BIOS - the basics
Flashing a motherboard BIOS can be difficult, but if you take precautions you will have a much better chance of success.
One thing I should perhaps address related to flashing a motherboard BIOS, is to remove/disconnect as many devices as possible, in addition to default setting the BIOS/CMOS, to negate potential issue which may be involved when the first reboot after the flash is done.
To completely clear the CMOS, diconnect the computer from ALL power. Make sure you ground yourself first, then clear the CMOS by using the motherboard jumper, or removing the CMOS battery for 10 minutes, or what has been supplied to do so.
A previously recommended activity, was to only leave the floppy drive connected, the keyboard, and a 8bit or 16bit video card attached, though with the advent of PCI video, that was changed as most had none of those older cards, and VESA standards were [by then] supported in the PCI/AGP video and BIOS.
For newer computers, without floppies and/or with in BIOS flash, these issues have once again become at issue when motherboards are flashed. It appears when flashing these boards, ANY error becomes difficult or nearly impossible to recover from.
Don't set ANYTHING after that first reboot, but SAVE the CMOS settings and shutdown after it re-boots. Disconnect ALL power again, re-install/re-attach all the devices in the same slot order [to negate difficulties with the OS], reboot, then carefully walk through the prior specialty settings. ONE AT A TIME, saving after each change, NOTE whether POST shows the devices again. If not then modify to the proper settings.
This is because these areas may also have been modified OR changed.
Regarding the flash, if not BIOS instituted {newer boards}, the separate flash tool/file usually has a switch to save the present BIOS to a bin or other file, do so if possible. Sadly many make that information hard to find.
If this is done, then one can roll-back to the older BIOS IF you also over-write the Boot code.
Flashing to support larger hard drives.
It revolves around the ATA/ATAPI standards that have been created and chips which have this support HARD CODED into the actual adapter chip. The BIOS is then created to support the chips supplied upon the mother board. If the chip set has no support for a newer standard {way of addressing/translation} then nothing can be done to circumvent that limitation at the hard coded level as the on-chip translation can not occur without that built-in support. Flash upgrades for the BIOS or device, however, may include code changes which CAN be supported [chip-wise], but may not have been available or were improperly coded when originally released.
Referencing:
http://www.t13.org/ - the master site
http://www.t13.org/Standards/Default.aspx?DocumentType=3
http://ata-atapi.com/
http://hddguru.com/content/en/documentation/2006.01.27-ATA-ATAPI-7/
http://hddguru.com/content/en/documentation/2006.01.27-ATA-ATAPI-5/
http://www.pcguide.com/ref/hdd/if/ide/stdATA4-c.html
http://www.storagereview.com/guide2000/ref/hdd/if/ide/stdATA4.html
The only way to consistently over-ride the limitations is to add an adapter which provides the newer standards/translation, and a device which also supports the target standard or newer.
Certain issues related to OS support can be addressed via modification to drivers or additional software which provides that support, however, without an adapter/chip set, which also supports the newer standard, these generally provide limited support [all functions are generally not supported]. NOTE though that tweakers have found ways to manually modify some of those limitations in the BIOS via various tools which I will not address here.
IF the motherboard can not be flashed to support the ATAPI/IDE {PATA} hard drive, then you are generally limited to using a drive-overlay [preferably manufacturer supplied] or using a separate adapter which supports the drive.
SATA {serial ATA} drives can be added to older boards, but only if an adapter is used. This provides the translation which the Motherboard BIOS does not have, as well as the connection point.