I have no idea if this would work in your situation... but I have a plugin which has Windows and Mac versions but won't survive the translation from a Windows project to a Mac project without becoming crash-prone and throwing out lots of error messages.
What saved me was the script "ft-Effect Instance" on AEscripts.com. It makes a duplicate of an effect instance and its settings (either by copying the values or by expressions.) Possibly if you used it, it would keep the settings, but insert the newer version of the effect.
You'd still have to do the process on each and every instance of the effect, but it might save you from having to copy all their settings. But given your mention about not being able to copy and paste settings, I don't know if it would work.
http://aescripts.com/ft-effect-instance/