I would always use the "add" parameter when adding new vlans to the list . Below is the answer I think you might be looking for.
STP Configuration Guidelines
If more VLANs are defined in the VTP than there are spanning-tree instances, you can enable STP on only 64 VLANs. The remaining VLANs operate with spanning tree disabled. If the number of VLANs exceeds 128, we recommend that you enable the MSTP to map multiple VLANs to a single spanning-tree instance. For more information, see the "Configuring RSTP and MSTP."
If 64 instances of spanning tree are already in use, you can disable STP on one of the VLANs and then enable it on the VLAN where you want it to run. Use the no spanning-tree vlan vlan-id global configuration command to disable STP on a specific VLAN, and use the spanning-tree vlan vlan-id global configuration command to enable STP on the desired VLAN.
Switches that are not running spanning tree still forward BPDUs that they receive so that the other switches on the VLAN that have a running spanning-tree instance can break loops. Therefore, spanning tree must be running on enough switches to break all the loops in the network; for example, at least one switch on each loop in the VLAN must be running spanning tree. It is not absolutely necessary to run spanning tree on all switches in the VLAN; however, if you are running spanning tree only on a minimal set of switches, an incautious change to the network that introduces another loop into the VLAN can result in a broadcast storm.
Note If you have already used all available spanning-tree instances on your switch, adding another VLAN anywhere in the VTP domain creates a VLAN that is not running spanning tree on that switch. If you have the default allowed list on the trunk ports of that switch, the new VLAN is carried on all trunk ports. Depending on the topology of the network, this could create a loop in the new VLAN that will not be broken, particularly if there are several adjacent switches that have all run out of spanning-tree instances. You can prevent this possibility by setting up allowed lists on the trunk ports of switches that have used up their allocation of spanning-tree instances. Setting up allowed lists is not necessary in many cases and can make it more labor-intensive to add another VLAN to the network.
Spanning-tree commands determine the configuration of VLAN spanning-tree instances. You create a spanning-tree instance when you assign an interface to a VLAN. The spanning-tree instance is removed when the last interface is moved to another VLAN. You can configure switch and port parameters before a spanning-tree instance is created; these parameters are applied when the spanning-tree instance is created.
