New Azure AD Connect does not have any impact on existing ADFS/WAP infrastructure. Azure AD Connect is completely separated from it. Azure AD Connect can be used to simplify some operational tasks on your ADFS infrastructure like initial config, creating necessary claim rules, updating certificates, etc., but even this is not mandatory - you can do the changes manually directly on the ADFS/WAP servers.
So, simply said, you can deploy new Azure AD Connect and you don't need to do any changes on your existing ADFS/WAP servers.