Importing a GenericSetup profile always runs all steps. For steps controlled by something in the file system, this is no problem: put into the "profile" folder only things for steps you want to get run. Generic handlers typically explicitly look for a file in the profile directory - just to let a profile control whether the step should do something.
You need to write an upgrade step, search for all contents with the related interface. Then you iterate over the results and update somesettings as needed.
from collective.example.interfaces import IMyInterface
from plone import api
catalog = api.portal.get_tool('portal_catalog')
brains = catalog(object_provides=IMyInterface.__identifier__)
note: I typed it directly here on the reply box, so there might be typos