I did it last night. Switch #2's config was lost. Since it was all the same VLAN except for 2 ports it was a relatively simple rebuild. Also one of the VLANs on switch 2 did not exist on switch 1, so it had to be defined. In retrospect it makes a lot of sense.
There is something in the documentation about backing up/writing individual unit configurations so I might have been able to 'inject' the old config back in, but for me, setting 46 ports into one VLAN and two into another was the approach to take.
Thanks