@Simon Belmont, Thanks for posting in Q&A. Based on my checking, the Custom-URI ./Device/Vendor/MSFT/VPNv2/{ProfileName}/ProfileXML has action replace. We can update on the custom profile to replace with a new value in theory.
Here is one I test before:
https://learn.microsoft.com/en-us/answers/questions/64671/updating-vpn-profile-through-intune
I notice you have upload new xml but not working, please also change the profile name, sync on device side and see if it will be update on the device side.
If there's any update, feel free to let us know.
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