I think forget about the idea of a single schematic with two boards where each board has only half the components placed. Every time you run a rule check, you will be flooded with irrelevant errors, and it will also see the connectivity that belongs on the second board.
All of these are issues that can be worked around, but it seems like a messy approach.
Two projects is probably the simplest solution.
Otherwise you can also lay out the two break-apart boards side-by-side, and you could actually get them manufactured like that. It could save board manufacturing costs.
Richard.