This can be done, I don't think it is a recommended way of working, you'll however have to be focused to do this, although its rather simple.
Capture always creates a netlist from the root folder (the folder marked with a \ inside the project manager) and all the way down in the hierarchy. So you could simply make sure that you don't reference board2 from a hierarchical block inside one of the schematics inside board1 folder.
To create a netlist for board2 - select folder board2 and right click->Make root - this will ensure that only the hierarchy that starts at the level Board2 is netlisted - now go to tools, create netlist and do your netlist.
To create a netlist for board1 - select folder board1 and right click->Make root - this will ensure that only the hierarchy that starts at the level Board1 is netlisted - now go to tools, create netlist and do your netlist.
You would need to establish connectivity between the 2 boards through connectors. Also notice that if you use CIS the part manager will only show data for one of the designs at a time.