Соответственно и у той и у другой части будут свои вектора прерываний, ремап векторов делается 1 командой.

А можно подробнее, какой именно, командой делается ремап?

Bits 1:0 MEM_MODE[1:0]: Memory mapping selection bits
These bits are set and cleared by software. They control the memory internal mapping at
address 0x0000 0000. After reset these bits take on the memory mapping selected by BOOT0
pin and nBOOT1 option bit.
x0: Main Flash memory mapped at 0x0000 0000
01: System Flash memory mapped at 0x0000 0000
11: Embedded SRAM mapped at 0x0000 0000

Пример смещения векоторов на 32к во флэше.
NVIC_SetVectorTable(NVIC_VectTab_FLASH, 0x0 + 0x8000);

stm32f0 вроде не Cortex-M0+. Так что NVIC_SetVectorTable не годится.

To build such application, some special configuration has to be performed:
1. Set the application load address at 0x08003000, using your toolchain linker file
2. To be able to serve the application interrupts, you need to relocate the vector
table (which contains the interrupt handlers). However, unlike CortexM3 and CortexM4,
the CortexM0 processor do not support vector table relocation (it is fixed at
address 0x00000000).
A solution will be to relocate by software the vector table to the internal SRAM:
- Copy the vector table from the Flash (mapped at the base of the application load
address 0x08003000) to the base address of the SRAM at 0x20000000.
- Remap SRAM at address 0x00000000, using SYSCFG_MemoryRemapConfig() function
- Then once an interrupt occurs, the CortexM0 processor will fetch the interrupt
handler start address from the relocated vector table in SRAM, then it will
jump to execute the interrupt handler located in the Flash.
This operation should be done at the initialization phase of the application.