I just installed CB 17.12 on a Windows machine, and it seems that there are some useful changes. Now a clean does remove the .mod files, and the priority weights for the 3 source files in my simple test were automatically given values 0,1,2, ensuring the correct sequence of compilation. Maybe the resetting issue will also be fixed. (I assume the behaviour will be the same on Linux.)
I am attaching the 3 source files and the project file so that you can see what Fortran modules are, in case you are interested. The .mod files get created in the same place as the .o files (obj\Release in this case.) If you clean then try to compile amod.f90 you'll see that the compilation fails because the file bmod.mod, needed by the 'use bmod' statement is missing. Building the whole program works fine because the sequence is bmod.f90, amod.f90, main.f90.