Dail,
Thanks for your help - I guess the final question is, can a plugin transfer a file to another running NPP instance?
Another solution would be a new command line option to stop that instance receiving additional files in this way.
I mean, the compare plugin is really useful, and it is nice to use it from within NPP rather than using a different tool. However it is easy to get in a tangle if you use it in conjunction with other editing tasks.
David