Is there any way of just backing up the flash drive
This question has been asked so often in the forum. You can make a copy with dd or any other image copy utility. Please use the forum search too.
Or here: Solution to common problems
Every time the power goes out, I lose the server setup. I have to re-instal the entire server, remount the drives, recreate the shares. Go back in to windows and re-map the drives
Sounds like a counterfeit SD card faking higher capacity than it has. So all your writes go to nowhere but as long as the RPi is powered the stuff lives in the filesystem/page cache. Once you reboot everything has gone.
The readme.txt at the download location points to this thread where it's written: It's strongly recommended to always test your SD card with either F3 or H2testw first to check for counterfeit/broken cards.
BTW: 3 disks connected to an RPi are 3 too much 
I agree with tkaiser. This sounds like your SD-card. Whether it's a fake or not, they can fail and do weird things in the process.
You should have two, one working card and another card for system backup. (It's easier to clone an SD-card, then to rebuild.)
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