When the data directory is set with the environment variable p3d_data_path, and one selects "Option"->Select a different output directory", the initial (input) data path is set to the new output data path.
I don't really follow: how did you notice this and why does it bother you?
My usual way is:
- use a separate dir for raw input files
- set this dir with p3_data_path
- start p3d
- set the output dir (somewhere different)
- now the original data path is lost.
It bothers me especially if they are on completely different paths since I have to navigate through the whole file system.
This is actually more of a feature. This might be changed, in the future.