The only way is to remove the VM from vCAC database. Check the below KB where its explains.
"Removing a virtual machine from Management in VMware vRealize Automation"
Another workaround is change the vSphere agent behavior to move vRA destroyed VMs to a folder, instead of delete from endpoint.
Example: Place Destroyed Machines in a Folder
Type the following command to change deletion settings such that destroyed machines are placed in a vCenter Server folder, VRMDeleted, instead of immediately deleting them in the vCenter Server (the default).---
Senior Infrastructure Specialist