Search Directories are a station thing. They are not specific to a sequence so therefore I'm not sure exactly what you want is available.
Managing Search Directories in TestStand can be a challenge. I have a couple rules and tips:
* Always as the first directory on the list I have Current sequence file directory with Subdirs checked. Then any specific code module for that sequence goes in the same folder under SubVIs or CodeModules.
* My second directory always points to a shared location where I have code modules which are shared by all sequence files.
* All non-native dependancies will be in those locations.
* Other than that all other search directories are default to what was installed with TestStand. (unless I am proving something out, then I immediately change them back)
One thing you could do is in the Sequence File Load callback place some code that will set the search directories to be what you want for that specific sequence file. Then every time you load the sequence file it would change the search directories so that they "fit" that file. The problem is that if you load both files at the same time then try to run the one that was loaded first you could run into some issues.
Hope this helps,
