Arrested in 1942 on political charges, Merzhanov continued professional work as a sharashka architect, designing numerous public buildings in the Black Sea region, Krasnoyarsk and Komsomolsk-na-Amure.
Ditangkap pada 1942 atas dakwaan politik, Merzhanov masih melakukan pekerjaan profesional sebagai arsitek sharashka, mendesain sejumlah bangunan umum di kawasan Laut Hitam, Krasnoyarsk dan Komsomolsk-na-Amure.