If you can not re-load your incomplete downloads, it is because they were cancelled or because the incomplete folder had been deleted or emptied or it has been moved. I didn't delete anything is a natural excuse for why they are gone. They were deleted, that simple.
As far as where are they (downloads) going. Look at the new folder you accidently made in limewires root folder. if that is not the case they are going to the new folder you made somewhere. if they are not there(in your computer) you don't have them. If you wait days and weeks for a download to continue, most often it NEVER will. Just take the time to download a better version or file. I have been using peer to peer for years, since before the internet. when my files are gone, I did it!
if the program is failing, it is usually a wrong link ie I set my download options to a wrong place. The best alternative is to clean up the incomplete, clean up all references o limewire or program, reinstall it with the newest version and start over. Why waste time fixing something I broke. clean up, reinstall and watch where I save and what the error messages tell me I am about to do wrong.