After you disable the zonning configuration on the new switch the active/effective zones woult still remain part of defined zoneset. Once you merge it with the fabric the new switch will receive the effective zonning information from the Fabric, however it will retain the old zonning information as defined configuration, this will not be added to the effective zonning, automatically. Thus you are right that the zonning information remains in the defined zonning on the new switch.
In case you are looking for the zonning from both the switches to be part of the effective zoneset, I would suggest you to follow the recomendations listed earlier :-
If you want the zoning data from both the switches to be there in the entire fabric then for them to automatically merge the conditions are:-
1). The alias names, zone names, and zone configuration names on the new switch and the fabric must be unique (the zone configurations must be completely different), or
2). The zone configurations on the new switch must exactly match the zone configurations of the fabric.
So for both zoning cfg sets to merge automatically you will have to ensure that all the zoning objects are unique and let the cfg on 48000 remain enabled and disable 4100's cfgset (using cfgDisable command on CLI) before merging. Else it will result in fabric segmentation and you will have to merge zoning data manually. Ensure that you take a backup of Wendy's Customer Survey the configuration on all the switches, just in case you may need them in case of some error. You should have scheduled maintenance window for all this activity as there may be some disruption due to zoning cfg changes.
Hope this answers your queries.