Answer Description

Resetting the CMOS battery will clear any saved BIOS configurations and the computer will instead use the factory default. BIOS settings are not managed in Windows and re-seating the HDD jumper will not affect the BIOS config.

Wikipedia

Nonvolatile BIOS memory refers to a small memory on PC motherboards that is used to store BIOS settings. It is traditionally called CMOS RAM because it uses a volatile, low-power complementary metal-oxide-semiconductor (CMOS) SRAM (such as the Motorola MC146818 or similar) powered by a small "CMOS" battery when system and standby power is off. It is referred to as non-volatile memory or NVRAM because, after the system loses power, it does retain state by virtue of the CMOS battery. The typical NVRAM capacity is 256 bytes.The CMOS RAM and the real-time clock have been integrated as a part of the southbridge chipset and it may not be a standalone chip on modern motherboards. In turn, the southbridge have been integrated into a single Platform Controller Hub. Today's UEFI motherboards use NVRAM to store configuration data (NVRAM is a part of the UEFI flash ROM), but by many OEMs' design, the UEFI settings are still lost if the CMOS battery fails.