I have a furnace with a 20 va transformer can I replace it with a 40 va?

Sure.

VA is volt-amperes, which is nothing more than AC power or watts.

The control circuit will have a certain load in VA, which is mostly the load of the relay coils. Also can be pilot lights, etc.

What is often often forgotten, is relay coils will have a steady VA once they are energized and in place, but the initial start of a relay coil is called "in rush" amps or VA. This happens quickly, (inverse time) or load reduces as time passes. This in rush load can tax a transformer if not sized properly.

In this case, bigger is better.