I have a 3 ph 120/208 400a main breaker. The line side conductors are parallel 4/0 ,2 per phase. Can I measure current on 1 conductor per phase or do I need to measure both conductors at the same time?
In the real world, there will be slight variations in resistance due to connections or slight cable length differences that will affect current flow in each individual conductor. Not much, but some. The best practice is to pass all of the conductors through the same CT window.
You can measure them any way you like... as long as you know how to manage your results.
If you can't get your clamp around both line conductors, measure individually and add... assuming the result for each holds steady while the measurement is being taken. If it is fluctuating all over the place, you're not going to have an accurate reading of either anyway.
Sometimes paralleled conductors can be 10% off more / less between conductors making up the set, depending on length.
Measure both initially and see if they are close enough to only do one and multiply by 2. It is more accurate to measure both conductors at the same time.