Andrew
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We do the same thing. We have one project for each environment, each with its own cluster. Unfortunately, we chose difference cluster names for each.
I wrote a small JS script that would change the cluster name in the "data_sources\mongodb-atlas\config.json" file. When pushing to a different project we change the connection in the APPSERVICES CLI and then run the script to change the cluster name. Then you can push.
Also had to extend the script to change the environment name setting in the root_config,json file.
Ideally need --cluster-name and --environment options for appservices CLI