Yep that will happen if LW crashes. The way to force the incomplete files back into the downld window is, go to LW's Library window, Select the incomplete folder, select the incomplete files, then press the Resume button. The only downside is that all incompletes will start from 0% no matter how much of the file had previously been downlded.

More about this here Downlds refuse to reload (click on link)

If this issue happens frequently then you should try to find out why. Also back up the incomplete preferences files perhaps daily or weekly depending on how often this issue occurs. The incomplete preferences are found in the incomplete folder & are called downloads.dat & downloads.bak
These files are vital & should normally never be tampered with. Just making a backup is different though. If need to use after a crash, before opening LW, replace the incomplete prefs with the backed up ones.