Do you know how the flash drive was partitioned before? The factory
setup was most likely one partition.
If all you did was write a new partition table, then all of your
files are still there. To fix this, you must restore the partition
table to what it was when you wrote those files.
I'm not a windows user, so I don't know whether whatever you used to
do the partitioning chose to be really helpful and zeroed out the FAT.
Using the same tool you used before couldn't make things worse.