One thing you could do is create seperate resource files for the files you dont what to share, which sounds like it would mainly be wdl files. Then, include those resource files in your game, this will leave all the other files open allowing you to do what you need.

However, according to the maunal:

"If a file with the same name is found separately outside the resource, the engine will use that one instead of the packed file in the resource – unless it's a script. Scripts must always be packed in the resource."