When vtp is configured, the configured vlans are stored in vlan.dat file, not in running-configure or startup-configure file.
It is common that two vtp server in a same domain is running, this is for vlans database redudant. When there is a new change generated in one VTP server, the update will be sent out inside the vtp domain, the other vtp server in the same domain will update its vlan.dat also.
Be careful to setup the same vtp version on both servers, otherwise the server with higher version will become master.
When replacing a switch that is acting as VTP server in the network, the best way is to change the new switch into client mode first, in order to get vlans updated from other vtp servers, then change the new switch back to server mode.