I am considering porting my E4 sampler library to Kontakt (via Halion) and have downloaded the online demo.
With the Emu EOS you can overlay a template (all filter, amplitude, EQ, modulation, continuous controller data, etc.,) on top of a mapped series of samples...and vice versa...place a mapped set of samples into an empty template. This makes setting up complicated instruments easy by working from a standard set of sophisticated templates (brass, winds, strings, perc., piano, etc.).
I have not yet found a method of doing this in Kontakt, and am wondering if I am missing something obvious. Moving bunches of samples around is much more time consuming than just superimposing a finished template.
In the current version of Kontakt you cannot copy groups with their according settings (effects, etc.). But you could copy your old instrument, delete all zones except one (for each group) and replace the samples zones. This way, the settings in your instrument should be the same for each group with exchanged sampes.