I don't know if Flash Tool will read a NAND that has been modified with ECC (which is what you would be reading off the board now if you flashed the ECC).
You can use a virtual nand with nandpro.
Make a COPY of the original dump and put it in the nandpro folder.
Instead of using usb/lpt use the filename.
So nandpro file.bin:
This will allow you to append the ecc to this nand file
nandpro file.bin: +w16 000.ecc
(Of course with the right file names)
Then compare this virtual nand with what you have been dumping off of the console. If they match, life is good
FYI, I just tested this by patching my original nand with my ECC. 360 flash no longer reads the nand, it says invalid. So I would say it is likely you are okay, BUT follow the procedure above and compare the new dump with that created virtual nand. The last thing you want to do is lose your original NAND!!!!!