iPad iOS Version 4.2.1
GoodReader v 3.2.0

Update 02/03/2011
I think I found a solution using i-Funbox to find and rename the application directories on the iPad.
Running i-Funbox in Windows and searching for "Goodreader" I found my files on the iPad under:
//var/mobile/Applications/
and a newer, emptier GoodReader folder under:
//var/mobile/Applications/
This second is dated 02/23/2011.
The first is dated 12/09/2010
So I renamed the folders (closing iTunes first, just in case) and when I re-launched iTunes, my GoodReader Documents folder had all those documents that were missing!
Next to try the same with Stanza, which has suffered the same problem.
//var/mobile/Applications/474C8147-5774-43E5-A9BA-1D1AE21BA3EC
//var/mobile/Applications/4AEEF8C6-E2F2-4A2D-BAFF-9C796FE6BF66
Update 02/04/2011
It seems every time GoodReader is re-installed, it abandons the old path with all the files and starts over in a new path:
//var/mobile/Applications/6331B84F-781B-404E-83AC-A614792FD8AC <- old path with original files
//var/mobile/Applications/F1A3A766-ABA8-47CD-97C6-EE09FA4D8BB0 <- new path after reinstall
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