This is exactly what I did last night. I figured it would be easier to download the game to system memory because I can always rely on that more than anything else considering there might be some issues with the drive falling asleep, using stand by mode, or whatever.
I found a useful website page online that said it would be best to copy games over from the hard drive to the system memory, and delete all the data except for the save data. That way if anything in the hard drive fails, I will always be able to redownload the game from the eShop and pick up where I left off.
There is still this cloud of anxiety that hovers over me everytime I load up a game from the USB Drive, though. But so far so good today. I have rebooted my Wii U on several occasions and loaded several games just to see if something messes up, but I can't seem to get it to malfunction like it did these past few days.
I hope it really does work. Not having to buy yet another hard drive (which could also have the same problems as the one I have) just to play the 50GB or so of games I have downloaded would be really, really nice.
Thank you for the help. I really appreciate it.