I think you will run into problems with the migration if you just accept those specific warnings. I imagine if it thinks NSX-V isn't installed it won't run the uninstall-V / install-T process correctly as part of the migration coordinator.
Which versions of NSX-V and NSX-T are you running/migrating to? The migration coordinator is limited to NSX-V versions 6.4.4, 6.4.5, 6.4.6, 6.4.8 and above. https://docs.vmware.com/en/VMware-NSX-T-Data-Center/3.1/migration/GUID-8C3E2019-D5A9-48F6-B9EC-A9E91...
