When you run mypyc to compile a set of modules, these modules form a compilation unit. Mypyc will use early binding for references within the compilation unit.
If you run mypyc multiple times to compile multiple sets of modules, each invocation will result in a new compilation unit. References between separate compilation units will fall back to late binding, i.e. looking up names using Python namespace dictionaries. Also, all calls will use the slower Python calling convention, where arguments and the return value will be boxed (and potentially unboxed again in the called function).
For maximal performance, minimize interactions across compilation units. The simplest way to achieve this is to compile your entire program as a single compilation unit.