The main config will not change, if you renumbering the switches - and rebooted - example as below :
Switch 1 now Gi 1/0/1 - now changed to Switch2 - the port become 2/0/1
The respective config will not going to change.
So you need to change the configuration of G1/0/1 to Gi 2/0/1 - since this this physically connected (only logical number changed).
what ever config was applied on G1/0/1 to Gi 2/0/1 after change need to be change to work as expected.
If you see any loops - i suggest to shutdown the ports and change the config and enable (no shutdown for safer side)