A VLAN interface should only go down when there are no ports in that VLAN that are in a forwarding state. We would need to know more about the topology and configuration on the switch to give a better assessment of how to prevent a topology change from causing a VLAN interface to flap. In most networks, I would not expect a VLAN interface to go down due to a topology change. Mainly because there will typically be a good number of ports forwarding for any given VLAN.
If you've experienced aberrant behavior surrounding topology changes and VLAN interfaces going down, I would recommend opening a case with GTAC.
Escalation Support Engineer