FortiManager ZTP with FortiSwitch

We are deploying a lot of Fortigates with FortiSwitch and FortiAPs with FortiManager.

Using pre-run scripts which creates interfaces and zones, so that we can apply SD-WAN template, policy packet and post-run scripts to update the interfaces with the correct data. All this works perfectly unless there is a FortiSwitch connected. 

If there is a FortiSwitch connected the above fails since it´s trying to remove the Fortiswitch configurations, which is automatically added when a switch is detected. If we also add the switch in the pre-run it works but we don´t know which switches is going to be on each site so we need to solve that so we can achieve almost a ZTP.

Any ideas on how to solve that?