I used to use synctoy, and another one allwaysync.
There fine but can lead to issues, if you make a mistake configuring them, especially the more complicate "propagate deletions and such.
With Backups, I think the best solution is the simplest one. ie the way you did it before, copying library to an external.
Using 2 flash drives may be overkill?
I'm assuming you worried about loosing the library, after deleting it and before writing the new version - if so, just copy it to your HD first, then delete and copy the new one to flash.
If you want 2 flash drives to store one somewhere else then ignore above.
Alt:
Dropbox with free 2GB storage
Skydrive windows live - free 25GB
Always a good idea to stick a copy of your library on one of those
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