The downloads.dat contains all data to resume a file. If you delete it, you can't resume.

If LimeWire crashes, the downloads.dat isn't written. The downloads.dat is being written when ever you add/kill a download (although the killed download is not necessarily removed from the downloads.dat) and when you close LimeWire.

When you mess around with incomplete files, and LimeWire doesn't find the incomplete file at some point, it deletes all resume-data from downloads.dat.

If you kill a download, the incomplete file is not removed, so don't play around with the temporary files.