I'm running in to this issue and I can't manage to find a solution. I have a workbook and I'm publishing it's datasource to the server, once the workbook is using the server's datasource I also publish the workbook to the server. Until here, everything works as I expected.
But then when I try to refresh the data periodically using the cli, the workbook in the server breaks because some of the calculated fields are pointing to fields named (sqlproxy.***) instead of the original fields.