Ken,
Have you closed out the program yet?
If you haven't close onecnc and restarted then you can use the "undo" button to get back to the point when there was NO fillet between the surfaces. Then it's just a matter of redoing the fillet to the new radius.
If you have restarted you will not be able to change the fillet, because as you found out when you disconected the surfaces, it has trimed the two or more surfaces in the fillet operation. And because the fillet needs to have two surfaces trimmed together or a solid model, so it can create the fillet, it will no longer fillet those features.
Bummer I know, but there is no way for the program to figure out exactly how to fillet the two together.
You will have to some how recreate the surfaces so they are trimmed together, by new surfaces or cut and merge operations, then you can refillet to the new size.
If you want me to take a look e-mail me the file.
Hope I explained this ok for you. If not let me know.