It may be possible to delete it manually from the config - take a good backup (with permissions/owners), shut down tvheadend, and wander around the config, especially ~/.hts/tvheadend/input/linuxdvb/adapters. That's where you have the adapter records that tie back to the networks and thence muxes and services. If you're changing to an adapter of the same type, or keeping the network/mux definitions for the old adapter, then this should be fine; if not, you may have some 'ghost' network definitions, but you can delete those through the GUI before you shut down if that's a risk (and likewise any surplus muxes).
Completely untested, it's just what I'd do... and probably break something, which is why the first thing you need is the backup :)
