Don't remove them then. You'll keep encountering these problems all the time. The thing is that (if I'm not mistaken) you still have the exploit in there, which causes the Wii to crash and thus, attempt to load your .dol file. I can't remember exactly what the name of the file and the directory the exploit is supposed to be in (only hacked one Wii, my Wii, and it was a long time ago, so I can't really recall it), but if someone else where to fill in... basically you just have to remove the exploit card from your SD and your good to go.
On the other hand... it'd strongly advise you to move (or at least copy) your bootmii files to a computer or another safe device. You never know if the physical integrity of your card can ever be compromised (having it break, melt, fall down a cliff or sink to the bottom of a lake), or if by some random odds, the data in your SD becomes corrupted (thus requiring for you, in most cases, to format it and lose everything you have in it).
Personally, I don't know why'd you like to keep your NAND backup with you at all times. Unless you were constantly tinkering with dangerous areas of your Wii, there really is no point in keeping it on your SD. Even I have limits to my bricking paranoia, heh. You could always go ahead and purchase a second SD card and use it for whatever mischevious things you want.
I hope I helped. If anyone else finds my post lacking, feel free to add what I missed.
Edited 1 time(s). Last edit at 09/12/2010 10:55PM by Magil.