Hi Chris,
You should be able to add the folder in which the copybook is actually located to the Dependency Path tab of the project properties and it should find the copybook even if it is referenced in the program with the E: in the name.
I just tested this here by placing copybook named copyfile1.ws into the folder E:\mycopys.
In my program I have the following:
copy "E:copyfile1.ws".
On the dependency path tab I added the folder e:\mycopys and when I compile everything is found without a problem.
Thanks