Well, that is exactly the reason why SD should not be formatted at all.
And if you really have to use the dedicated formatter from SDCARD.ORG
By the way: you theory is not correct
There is nothing to flash on a TT and the bootloader is only a file on the SD or internal memory - it is being installed into the resident flash memory of your device.
There is not interaction between SD and BL apart from the fact that is a file stored on the card.
It is not possible for a TT to create partitions, so I assume something went wrong on your PC rather than on the TT.
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