My courses uses javascript to make html files popup in new windows. When I publish the build as an AICC build. These files are omitted.

Is there any way I can keep files that are placed in the project source folder?

These will be files that the module refers to but aren't bits of 'courselab' itself.
When you build the AICC or SCORM it thoughtfully omits these but does retain the references to the files.
As these sound like a part of the module I'd suggest add these below the root level of the module while building and then reference them from within the module.
Once you generate the final output just copy the folder with the files over to the same level in the output files.
You need to watch out for other objects like this which can just disappear once you publish.