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If they werent pvs i would have you look at setting the autoupdate citrix policy to disabled which tells the vda to use the listofddcs before the controller cache. I guess i would still try it since you are having issues https://docs.citrix.com/en-us/citrix-virtual-apps-desktops/manage-deployment/vda-registration.html

I have turned off the on prem DDC's VM's and left it for 10-15 mins and the affected VDA's have now registered with the cloud connectors guessing it was using a cache of the controllers

Glad you got it