BOOST_PYTHON_MODULE(module_a) {
  boost::python::class_(A, .....);
}

BOOST_PYTHON_MODULE(module_b) {
  boost::python::import("module_a");
  boost::python::class_(B, boost::python::bases<A>, .....);
}

import module_a  # перед module_b
import module_b

PyFinalize Safety

Currently Boost.Python has several global (or function-static) objects whose existence keeps reference counts from dropping to zero until the Boost.Python shared object is unloaded. This can cause a crash because when the reference counts do go to zero, there's no interpreter. In order to make it safe to call PyFinalize() we must register an atexit routine which destroys these objects and releases all Python reference counts so that Python can clean them up while there's still an interpreter. Dirk Gerrits has promised to do this job.

К>BOOST_PYTHON_MODULE(module_a) {
К>  boost::python::class_(A, .....);
К>}
К>

К>BOOST_PYTHON_MODULE(module_b) {
К>  boost::python::import("module_a");
К>  boost::python::class_(B, boost::python::bases<A>, .....);
К>}
К>

auto module_a = boost::python::import("module_a"); // import before B
BOOST_PYTHON_MODULE(module_b) {
    boost::python::class_(B, boost::python::bases<A>, .....);
}
module_b["__imported_module_a"] = module_a; // dont know how exactly set the module attribute

static vector<tuple<string, so_handle, js_handle>> libraries;

// visible in all dynamic modules
[[dllexport]]
js_handle load_library(string name)
{
    js_handle = find(libraries, name);
    if (!js_handle)
    {
        so_handle = ldopen(name);
        js_handle = my_init(so_handle);
        libraries.push_back(name, so_handle, js_handle);
    }
    return js_handle
}

static void unload_all()
{
    auto unload_library = [](tuple<name, so_handle, js_handle> lib)
    {
        my_fini(js_handle);
        js_handle.reset();
        ldclose(so_handle);
    };

    std::for_each(libraries.rbegin() libraries.rend(), unload_library);
    libraries.clear();
}

int main()
{
   init_js_engine();
   js = load_library("main"); // may invoke other load_libray() calls
   run(js);
   unload_all();
}

python3 -c 'import module_b'

PM>Да обычно вообще динамические библиотеки не стоит выгружать пока работает программа