Two thoughts - neither original, but maybe a bit quicker:
Split the removed downloads file in half and put 50% back in the game - if it works the problem file is in the other half, or vice versa. Split the offending half again and repeat... its a bit quicker
Delphy's Download Organiser from MTS2 makes orgainising your downloads easier - still a pain but easier.
Of course if you are certain its one particular download I'd remove and redownload it.