And that's why you always work in KVA; KVA does not lie, and it is not distorted by voltage changes. KVA is KVA.
If the panel schedule is totaling amps, it is junk, don't use it.
It sounds like you may be trying to use individual load amps and trying to add them up, when in reality you need to add kVA's and then calculate current.
Even when you use kVA the question comes up (and I think it is the one the OP is asking about) of what to do with line to line loads.
The answer, which gives you the right overall load on the panel and allows you to work your way back to the source to see if adequate KVA is available is this:
Whenever you have a line to line load, assign 1/2 of the load kVA to each pole/breaker. That way when you add up the kVA loads on each phase and then add up the 2 or 3 phase kVA values you will end up with the sum of the load kVA values and not twice that number.
The proper calculation the of the current for each bus or feeder line is subject to disagreement when severely unbalanced loadings are present. Just taking the total kVA and applying the three phase current formula does not give you the same answer as adding up the kVA assigned to each bus and dividing by the line to neutral voltage. The NEC does not seem to care about that.
Accept it.