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Found this post while perusing eQUEST/doe2 related queries some time later... surely too late to help with this project directly but I can answer for the record if anyone else has a similar query:
The 'easy' response to achieve the intended effect for the purposes of calibration would be to (A) not combine the two existing DOAS systems (so split them up, permitting the assignment of unique FAN-SCHEDULEs), then (B) creating a "broken" FAN-SCHEDULE forcing non-operation for the requisite 6 months out of the year (using days with all zeroes for the hourly ON/OFF/FLAG input).
An ECM to resolve that issue, thus providing the amount of OA intended by the design, could then simply swap in the "normal" fan schedule that's assigned to the other DOAS for each run.
Hope that helps someone moving forward!
~Nick