revisions and different sopc

How are you creating the SoPC systems. Are you launching SoPC builder directly from Quartus (In which case SoPC builder is aware of your Quartus project and generates its files directly in your project directory) or are you using the megawizard plug-in manager to launch SoPC builder (in which case SoPC builder is unaware of your Quartus project and can be located anywhere in your file structure).

I would create two SoPC systems in two different folders using the megawizard method. Then I don't think they will be aware of each other.

FYI. I believe the JTAG node instance can be overridden using a parameter assignment to the appropriate design entity.

Jake