Interim commissioning whilst renovation continues?

[cloughapike]

I installed our Flair MVHR unit (ages ago) and have slowly added pipework as rooms have been renovated and was not intending to commission it until all were finished, but as we are now inhabiting most of the house most of the time and have a working kitchen I definitely feel the need for better ventilation.  Is it OK to balance the system as it is now then re-balance it once the final rooms (a bedroom and bathroom) are renovated? I intend to cap the pipework to these two rooms for the moment.