After you start an end-to-end migration, do not change the NSX-V environment. If you want to deploy VMs during the migration, wait until some of the NSX-V hosts have migrated to NSX-T and deploy the VMs on NSX-T hosts. Connect the VMs to NSX-T segments and install VMware Tools on the VMs.
Deploying on NSX-T with VMware Tools installed ensures that the VMs are populated into security groups and receive the intended Distributed Firewall policies.
VMs deployed without VMware Tools installed, or deployed on NSX-V do not receive the intended Distributed Firewall policies.
If you use vSphere templates to deploy VMs, update the templates to use NSX-T segments for the VM network configuration. Specifying NSX-T segments ensures that any VMs deployed using the templates are deployed on NSX-T hosts.
If you use automation tools to deploy VMs on vSphere, but do not use vSphere templates, you might need to change your automation tool configuration to ensure that the VMs are deployed on NSX-T.