Always be sure to properly remove the hardware from your computer. When removing from the wii I always make sure it is fully shut down before I unplug the hdd from the wii.
When putting my backup games onto my USB either using USB Loader/Configurable USB/Wii Backup Manager etc. Sometimes there's a chance that my USB becomes corrupted, and only the last few games will play, and to fix this I'd have to reformat my USB using the Fat32 guide and start over.
I currently want all my games on my USB, but this has become troublesome since sometimes I have to reformat in order for it to even work again. And then once formatted, sometimes it does it again (randomly corrupt files). When doing this, certain files no longer appear. So if I backed up lets say 4 games, once it gets corrupted, only 1 or 2 games show on my USB and the other 4 games that used to work perfectly won't work anymore unless I reformat and start the process over.
Is there anyway to prevent this?
Your computer should have some tools to attempt to repair the corrupted drive. Not sure what exactly it's called on Windows(I'm a GNU/Linux user) but a quick Google search should get you the information you need. Also, run a SMART check on your drive (if it supports it) to make sure nothing is wrong with the drive itself.
SM 4.1 (v499) - BootMii/IOS v1.5 - HBC 1.1.2 - Priiloader 0.8b6 - d2x v9(r49) - WiiFlow 4.1.1
[SPOILER=Must read threads]Thinking About Hacking a Wii? Read This First.
Softmod ANY Wii (updated 03/30/2013)
How To Run & Post A System Check[/SPOILER][SPOILER=Helpful threads]USB Compatibility List
Troublesome Games And Their Solution
Originally Posted by sven
Yeah, this sounds like you may have some corruption on the drive itself. If using Windows, go to the start menu. In the search box type in chkdsk e: /f
Replace e: with the drive letter corresponding to the drive letter of your Wii drive.