This happened to us about 2 or 3 years ago so things may have changed but.....

Flying to BOM on an AF codeshare connecting to a Jet flight to KTM (separate ticket). Business class. We were identified at the exit of the BOM arriving flight and escorted to a waiting area. An AF person took our passports and bag receipts and while we waited airside cleared us through I&C, got the bags and rechecked them at the Jet counter.

This may or may not happen for you (call VS and ask) but it indicated that we would indeed have to clear customs, exit, recheck, and clear security back into the terminal. Things may have changed but call anyway.