It is not always needed to restore the baffles, especially if you chose to use modern pistons and rings. Sometimes welding baffles in place can warp the cases and induce more machining work than it is worth.

It's another matter with the flywheels. It isn't always needed to replace a flywheel even it it has been in a breakdown. It can be marred at the edge without compromising strength. However the Indian windowed flywheels are notoriously weak at the tapers and crack easily when reused, trying to torque nuts to final specifications (According to Service Shot No. 141-April 11 1944, not more than 75 fp-lb=101 Nm=10kg-m!) 

I recommend always to replace windowed flywheels for new repro steel  flywheels because a flywheel breakdown is mostly sudden, final and very unhealthy in the case of a fall on the road at speed. Steel flywheels withstands easily (100 fp-lb=135 Nm=13,7 Kg-m) torque on the nuts and are in most cases easier to true up.

In a pinch use the newer Scout flywheels that does not have windows but still use the lower nut torque on those. Even better is to use Z marked flywheels that are cast steel and can take the higher torque.