I don't know what you did to "reconnect" but what probably happened is, that there are two files with the same filename but different SHA-1 hashes, - since those files differ (although it might be just one byte that is different) LimeWire will create a new incomplete file for the second file and start at zero again. If it encounters the first file again, it will continue the first download at 99%.

Another possible explanation (if you killed it and resumed it for example) is that you messed the download up and LimeWire "forgot" about the original incomplete file.