I'm unsure of your question. Please clarify ... Are you trying to search for an assy within a common directory, or are you wanting an assembly to search for its component parts within a common directory?
Have parts or folders been moved, or renamed?
Tools > Options System Options > File Locations > Referenced Documents sets the document locations.
In SolidWorks Explorer, Options > Search sets the paths for the search function.
I placed only the main folder in the reference documents. How can I make SW search it's sub-folders? Is there some code like "J:\Parts%%" ?
Retrieving data ...