CheckBook Pro lets users save documents (data files) wherever they want, so the save location for your primary document would've been set whenever it was created. The first thing to do when data appears to be missing, though, is open the app, head to the
File menu near the top left of your screen, go to the
Open Recent submenu, and try each document listed there to see if all of the missing data then reappears. If that doesn't help, check out all the possibilities at
https://www.splasmata.com/?p=3123 — there's a section toward the bottom that covers how to gather recent CheckBook Pro log messages, and sending those to us via email ought to help us determine where any documents you've viewed recently were located at the time they were opened.