Is it safe to store the only copy of your Keystore/JSON file on a flash drive? I am currently using this method
No. Flash drives can potentially break by:
Leaving them for a long period of time. Flash drives have some deterioration over time.
Other physical damage
If you want to use flash drives, at the very least you should store the files multiple times on multiple flash drives. I would recommend also burning it to CD and/or DVD.
I personally prefer writing down the JSON on pieces of paper. It takes some time, but it's a good way of knowing for sure that you won't lose it.