So if i understand correctly the new physical management server will be running windows with all vCenter components (SSO, inventory service, DB etc) running on one physical server with the x3 ESXi hosts running the workload VMs?
If that's the case then yes but there's no need to rush to delete the vCenter Appliance. just power it off in the first instance, build your new physical vCenter, add the hosts back into the New VC (you'll get certificate errors but just continue through them).
Once you're back up and running then delete the vCSA.
Consider that you can't move the vCSA DB to the new Windows based vCenter so you will loose your performance data history, you'll need to re-enter your product keys and if you're using certificates from an external CA you'll need to configure those again also.
Also if you're using the VDS virtual switch you will loose that configuration also (unless you back it up separately) and any VMs running on that switch may loose connectivity. If you're using standard switches on your hosts then no problem as they are only local to the hosts and do not require vCenter.
But you won't loose any production VMs running on your hosts or even disrupt them.