Project layout - best practices

I’ve just taken over a project from a prior developer and am having difficulty getting a clean build process running (by build, I mean exporting for iOS or Android - the projects both come up OK within Fuse Studio). The prior developer created a directory structure with two projects (.unoproj files) in the same directory. The code for both these projects is almost identical.
The initial problem was that the content of the build directory collided - clean and build project A first then project B wouldn’t build and vice-versa.
I have created two build directories - build_A and build_B and and added an exclude in each project file to stop each project looking at the other build directory (to clean, I run ‘uno clean project_a’ etc.). However, the build still does not work correctly.
What would be the recommended way to structure dual projects like this?