Use FO3Edit's "Clean Masters" option after R-Clicking the plugin in the left panel. Provided there are zero references to any given master in the plugin's masterlist, the extraneous master(s) will be removed while keeping everything else intact. If "Clean Masters" doesn't remove a master, you'll have to track down the references to it and remove them or manually remove the master from the masterlist, but that's risky as you can easily bork your plugin.
I'd have to see the plugin to tell for sure, but it sounds like you're trying to merge RH and EVE together to work with FWE minus dependency upon RH and/or EVE? If that's the case, I'd start over and just merge one into the other.