When editing constraints using the PlanAhead tool for a Project Navigator project which has multiple UCF files, I am prompted to select the UCF file that I want my constraints written to. I make changes to my constraints in the PlanAhead tool, then Save and Exit. If I compare the timestamps of my UCF files, I see that both were rewritten. Why is this? Is this expected behavior?
Yes, this is the expected behavior. The PlanAhead tool's constraints database keeps track of all constraints, not specifically which constraints are modified. When the project is saved, all constraints are rewritten to all UCF files in the Project Navigator project.