I have noticed two reason why you should remove downloads from LimeWire's download list first before deleting from the Incomplete folder on your hard disc. One is that your Incomplete folder will just fill up straight away again, and the other is that LimeWire's download list will still be as full and unwieldy as it ever was.

If you have things still left in the download list that are missing in the Incomplete folder, it seems LimeWire assumes you have suffered a catastrophic data loss on your hard disc. Rather than making you start each and every download all over again from scratch, it looks like LimeWire instantly creates a new empty file in the Incomplete folder for every missing download. It then carries on trying to complete the downloads as before.

Moreover, as long as the download list is still as large as it ever was, LimeWire will be slowed down as much as before. It tries to get mileage on each thing in the list.

Note that LimeWire has a built-in feature for taking care of all this in its own way, however. In its preferences, there is a maximum time to keep incomplete downloads. I can't comment on this feature, since I am one of those people who uses LimeWire in a way that defeats it. I queue heaps of downloads in frenzied fits and I adjust the maximum time in preferences to be really long so that I can keep trying to get those rare downloads that look really tantalising.