Regd. night cycle allowed in proposed & baseline energy modelling using ASHRAE 90.1 PRM

The temperature settings can vary during the night. THe only requirement is that the temerature settings must be the same in the baseline and proposed. Are you experiencing unmet load hours in the baseline or proposed?

If you are experiencing significant unmet load hours in the proposed this is an indication of one or both of two things, 1) there is a design flaw in the proposed design causing them, or 2) there is an error in your model causing them. You must have the same temperature settings in the baseline and proposed, so yes the same night cycle must be in the baseline. Also note that the proposed must be modeled as designed. So is a night cycle currently included in the proposed building's sequence of operations? If so then it is fine, if not then it is not modeled as designed. Submitting the schedules are not required but depending upon what the reviewer sees you might be asked to provide them for a final review.  

Typically the procedure is to incrementally increase the baseline simulated system capacities, and the baseline building resimulated until unmet load hours are reduced to 300 or less.

Do you have unmet hours for cooling or heating or both, and how many hours do you have? When i try to reduce unmet hours I usually check when and where the unmet hours happen. Here are two points that happens a lot -  Often times the space are not brought to the setpoint fast enough in the morning so you may try increasing/decreasing the unoccupied hours setpoints an hour before the actual occupied hours. For example it may be difficult for your unit to bring a 60F space to 70F within an hour, but it will be easier if the setpoint is 65F space to 70F. It may not be the actual design but if will make your proposed model energy more conservative. Does your simulation program allows you to check if the cooling/heating coils are hitting their supply air temperature target? if it fails it mean the proposed capacities are undersized. I will check with the mechanical engineer and see what internal gain assumptions did use. The occupancy density is often overlooked, the energy program's default density is usually based on ASHRAE 62.1 which maybe a lot higher than the actual design.   Good luck!