Freedom of movement is still in effect until the end of October, as for after that time the visa/residency question is up in the air but there's an extremely good chance residency of some form will be offered to British citizens who are already established in Germany.

As for the company being incorporated in what will become a third country, from my research I can't see any reason why that will fall afoul of any regulations (as long as everything is properly reported to the authorities).