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This may be a controversial suggestion, but here it is.. Your design is perfectly valid, but there is a limitation of the software engine that you're required to use. You might consider calculating what the average BHP would be using VAV fan controls, and then specify that in the software. Then use the "exceptional conditions" box to explain what you did. This is a reasonable energy modeling practice and you're up-front about it. Ultimately, it's up to the AHJ to review and approve the report but all the info is there so they can review and ask you about it (or deny it) if they so choose.

I personally wouldn't resort to something like that unless that is the change that makes the difference between complying or not. You'd want to have some backup on how you arrived at the average BHP - like using your VAV model and some hourly reports for airflow to determine how the fans would modulate, then apply the findings to the constant volume model.