Yeah, very easy - I’ve been doing exactly this for some time with great success. You’ll need to use Shrink for both sides - open the first side, process the movie down to what you want (remove unwanted titles & audio/subtitle elements) in “Re-author” mode by dragging the main title over as per normal & create an ISO. Then put in the second side of the disc & open it.
Switch back to “Re-author” mode & drag the main title over as before. Now, hit CTRL-I (you must have the latest version of Shrink to do this). This will allow Shrink to open an ISO file directly without having to mount it first. This will bring up a browse window - just browse to the location of the ISO you just created. You will then have to select “Re-author” mode again, which will bring you back to the disc project you just started a moment ago. You will have the new ISO open in the right window (you may have to select the “DVD Browser” tab to see it), allowing you to just drag the title across to add to the current project. Then just continue to finalise the project as normal.