You should be able to change the local repository folder but it's hard to say exactly what's going on here. One thing you could try is to change the log level for the VCS integration by entering the command "CALL LOGCONTROLLER('com.denodo.vdb.interpreter.execution.vcs', 'DEBUG')" in the VQL Shell. The logs will then record not just Errors but other information about what's happening as you try to change the repository path. If changing the logging level to Debug doesn't bring up anything obvious, if you have a valid support user, I would submit a new case to the support site so they can do a deep dive. Remember to change the log level back to "Error" with that same command when you've solved the issue to prevent performance problems from excessive logging.
For your more general question about on ensuring commits are deployed properly across different service, there's a great best practice guide to [Deployments and Continous Integration](https://community.denodo.com/kb/en/view/document/Denodo%20Deployments%20and%20Continuous%20Integration) that's a very good starting place.
Hope this helps!