Answered on the Official BlackBerry Java Forum: http://supportforums.blackberry.com/t5/Java-Development/Blackberry-Package-project-issue-1-debug/td-p/2508105
As requested, here are the important details from the linked post:
There is no corruption, what is happening here is that your project has got large enough to exceed the limits of a single cod, and so the project is being built into multiple cods.
Typically you don't see that, because the build process zips up the individual cods, and puts them all in one large cod. However the debug-n files are a good indication that you exceeded one cod file - these are always kept separate and there is a debug-n file for each cod file.
So take your single file ".cod", rename it to ".zip", and then open the zip file. You will probably see 2 cods in there.
Unzip this and put the multiple cod files on the web site for download. If you check the jad file that has been created, you will see that it lists multiple cods.
If you want to read more about this, search the BlackBerry forum for 'sibling'. The multiple cod files are generally referred as sibling cod files.
Also see here for more on this: http://supportforums.blackberry.com/t5/Testing-and-Deployment/The-maximum-size-of-a-BlackBerry-7-or-earlier-smartphone/ta-p/1300209