If I reboot my computer, any incomplete downloads that are not queued will be deleted from the Incomplete folder, and any that are queued will be reset to 0 KB downloaded.

This can happen IF you don't close LW fully down before rebooting, or your comp crashes.
My advice then is to make sure LW is fully closed before shutting down the comp. Also, go to your LW menu bar, Tools>Options>Saving & set Days to keep incomplete files to a large number like 999.

I doubt your incomplete files will actually be deleted. You can go to the LW Library window & select Incomplete folder & press the Resume button if they're not in the downld window. Do this if it happens again. But they may start from 0% so only do this as a last resort!

There was no crash. I shut down the comp without bothering to close Limewire... this had always worked perfectly fine before.

I have days to keep set to the max.

The files were gone, and due to the smaller size of the downloads.dat file, I assume they were deleted from there too.

How do you mean "the max" .. I set mine to 300 days which is a bit excessive but better safe....eh

2147483647 days. That's the max the field will allow. While I'm on dialup, I'm somewhat prone to start large downloads, get ~100 KB of them to ensure Limewire will resume properly, and then continue upwards of 3 weeks later. Like you said, better safe than sorry.