Hi Zhang126,
Even if that case, the process is same.
After merger of A&B, I understood the new Company name would be C.
Then you will have all your licenses, ISO 13485 cert on the name of C with address in Germany.
With the required applications/forms, ISO 13485 Certificate, you can submit the docs to your MAH of the Company A (now called Company C). He will submit to PMDA and all product notifications will be changed in registry.
Then, from my view, MAH of Company B will be dissolved. or C may want to have two MAHs in Japan!!
Regards,
Sreenu