CAESAR II only creates a PCF if you export the model to Isogen. The PCF will not affect the results. Depending on the size of the model, Isogen will break the model into several PCF files and related drawings. If you don't like this, you will have to use the "Edit Stress Annotations\Split", to define where you want things broken.

Rearranging a model to solve an issue, would overwrite an existing PCF.

You could always analyze disconnected systems. However CAESAR II should display a warning during the analysis that the system is disconnected.