VMs will not be affected from deleting the vCSA.

However, depending on which central functions are configured, you may need to be prepare the new instance before re-attaching the hosts to a new instance (e.g. distributed.switches, ...).

Although I think that you have this in mind, don't forget to reconfigure other things like backup, etc. after the setting up the new vCSA.

I assume that you don't have vSAN in use. In this case one needs to take a closer look at this.

André