If I am not completely wrong, I think I've read something about issues with older versions of the USBLoader (the one's below 1.5). If you delete a game with such a loader it can damage games already on the HDD and can currupt games that you try to rip to HDD.
I personally use WBFS Manager 2.5 (newer Versions available and working, I'm just too lazy to download and install it) to transfer games from pc to the HDD used with the Wii and vice versa.
For installing and deleting games directly with the Wii I use Waninkoko's 1.5 "original" Loader.
And for playing the games I have USB Loader GX.
Since I use them all in the desribed way, I never had any problems again. I remember having problems with installing and booting games when I tried to show my parents what the Wii is able to do when softmodded. I installed Twilight Princess from the original game disc to HDD, deleted it with Loader 1.1 and tried to reinstall it, to show how fast it works. After that i received some problems. I copied my isos back to my computer, reformatted my hdd with 1.5 and installed the isos back to hdd with WBFS Manager 2.5 (or 2.2, I don't remember...)
To cut a long story short...only delete and install games with Loaders based on 1.5 or they will mess up your hdd.
Amarabha