Nothing, an MD5 check is only so the PC can cross-reference the download to see if it has downloaded correctly.
For example, a download may have an MD5 of - 1122334455AA
If your download gets corrupted, it may have - 1122334455AB
Therefor the MD5 is wrong and the download is corrupt.
It will not affect your flash, it should just skip the check and carry on.
If the flash has gone wrong, perhaps the download is corrupt.
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