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Implement a different nand FTL with Flash file system

I'm using the ARM RL library for the Fat file system and flash translation layer (FTL)on a Cortex M4 MCU.
We need to implement a different FTL to support the NAND flash device we are using (better ECC and better wear leveling). That is fine, however we'd like to continue using the Keil FAT file system with it.
At what point in the code can I divert the FAT fs to our new FTL ?. The new FTL has the usual sector based interface.
Thanks.

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