Erasing the flash file system (FFS) is a matter of breaking into the debug session, preferably prior to the BSP trying to create the FFS. I like to set a breakpoint on customizeDialog; once the breakpoint is hit type the following command, at the GDB command prompt:
call NAFlashErase(0xXX, 0xYY)
Where 0xXX and 0xYY are the first and last sectors (zero-based) you wish to erase. What these values are depends entirely on the configuration of your BSP. By default a 256k (defined in customize.ldr) FFS is created. The FFS will be located in flash starting at the first secotor immediately following the application image. If for example your maximum boot loader size is 64k (defined in customize.ldr) and your maximum application size if 832k (defined in bootldr.dat) the FFS would be located starting at sector 17 (0x11) and end at sector 20 (0x14). This, as previously stated depends, entirely on your particular BSP configuration.
I would suspect, however, that FFS corruption is not, necessarily, your problem. From what example application, assuming you used one, did you base the FTP portion of this application? I ask this because some of the provided example application, naftpsvrapp for example, do not make use of the FFS. Instead they use a simluated file system, by way of a 2-dimensional character array; or in this particular application's case simply a large RAM allocation, into which your uploaded file is stored.