If you change a printer configuration through the http admin interface for CUPS, they don't show up in redhat-config-printer. A minimal step would probably to just detect that this occurred and put up a warning dialog.
This is generally hard to figure out. Some experimental code is in /usr/share/printconf/util/cups_import.py though. Try running that and see if it gives any good results. What changes did you make? Changes to a redhat-config-printer-managed print queue will get overwritten (don't do that); new queues should be unaffected (but the cups_import code could try to propagate it back).
(Incidentally, this will all get much better once we drop alchemist.)
What I did was to change a redhat-config-printer managed queue. Can we manage to somehow display in the CUPS admin interface "this queue was created by redhat-config-printer, editing is not recommended." or something?
How about if we put that in the 'description' field? Currently it just says 'Created by redhat-config-printer 0.6.x', but it can be changed.
Please take a look at cups-1.1.17-8, which has (I think) a neat way of doing this.