Sorry for the late reply, but here's how COMPAQ computers of the time work. The BIOS itself is on an EEPROM chip, as with other computers. With early IBM PC computers and compatibles, you'd do what's now called BIOS setup by setting jumpers on the motherboard, but then came jumper-less configuration, where BIOS settings could be saved on a SRAM chip, CMOS, powered by a CMOS battery to retain those settings. The software required to comfortably set up the BIOS would be too large for the tiny BIOS EEPROM, so computers came with setup floppies - you would boot off of them, set up your BIOS, then you were good to go.
Some manufacturers like COMPAQ came with a different idea - creating a hidden partition on the HDD, once HDDs got cheaper. The BIOS detects the presence of the so called "diagnostic and setup partition" and shows a prompt to boot to that partition. As HDDs allowed for a lot more storage, they also came up with very user-friendly and feature-complete Setup programs - not really for overclockers, but just a pleasure to work with.
When EEPROM storage got cheaper, most BIOS manufacturers integrated the BIOS setup in the BIOS chip - but it was still less than the storage Compaq could use on an HDD, so BIOS Setup programs did not usually have the conveniences of Compaq Setup&Diagnostics, like mouse support, Windows-like UX/UI, extensive diagnostic tools, etc.
The computer can actually boot and operate without the hidden diagnostics partition, but you will not be able to do BIOS setup.
To restore the hidden partition, you need to remove all partitions on your HDD, create setup and diagnostic floppy disks - there will be two or three of them - Setup, Diagnostics 1 and Diagnostics 2 - and booting off the Setup floppy will show the option to restore the Setup and Diagnostics partition. This can be done both on the old HDD and the new CF card.
I currently don't have a Contura 430C on hand - sadly, it was the first computer I owned - but you will need to dig into the ROMPAQs to see which one contains the setup and diagnostic floppies. As for the HDD support, mine came with a 420Mb HDD, and I think older COMPAQ bios had a bug which prevented it from working with HDDs larger than 4Gb.
Compaq Deskpro 2000/P2 300MHz/256Mb SDRAM/Matrox Mystique/Sound Blaster AWE 32 Value/Aureal Vortex 2
MSI 865P Neo/Pentium 4 HT 3.0GHz/512Mb DDR DRAM/GeForce FX 5500/Creative Audigy 2
Asus P5Q Pro/Core2 Quad Q9400/2Gb DDR2/GeForce 8800GT/Creative X-Fi