I have site to site VPN from my Azure VM to an on premise network. May I know how can I deploy the code on Azure VM such that the site to site network stays?
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Just for the sake clarity lets reiterate that A Site-to-Site VPN gateway connection is used to connect your on-premises network to an Azure virtual network over an IPsec/IKE (IKEv1 or IKEv2) VPN tunnel.
After site-to-site VPN is operational, network on both sides of VPN would be treated as one virtual network. This enables cross network accessibility of network resources as defined in access configuration.
Your questions needs clarity as I do not believe "the code deployment to a VM" would interfere "the network configuration" where the VM is housed.
It would be helpful if you could you add details to your question like error etc, in the meantime adding few pointers to get you started on VM creation and deployment.

Amit uchat
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