Alright, so I had a change of heart with every post being in DWF, but it remains a great tool and freewheel can be of great use for yourself and for clients, so definitely check it out.
So you are placing rooms in your phased building but you have rooms that are not effected by the phases, what do you do? Anybody who has experienced this has realized that rooms can exist in only one phase and you have to replace all rooms for any additional phases. The phases of rooms can not be modified and are set by the phase of the view placed in.
Option #2 and a huge timesaver is as follows:
1.) Select all rooms in your project that you want to maintain through the phase change.
2.) Click to the menu Edit -- > Copy to Clipboard
3.) Change to the View of the new phase of your building
4.) Click to the menu Edit --> Paste Aligned --> Current View
This will copy all of your Rooms and their parameters to the new phase of your project so you do not need to recreate the rooms for the new phase.