You won't loose any downloads by upgrading exept maybe if your download folder is in your Limewire program folder.

Go to library saved files and press explore to see which folder your downloads go to. Default would be C:\Documents and Settings\*Your Username*\Shared

If you haven't changed that then there should be no problem.

If on the other hand your downloads go to e.g. C:\Programs\Limewire\downloads then you should move them before upgrading