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I'm looking for an answer too on this, I've had the same issue trying to run this tool in cmd for different tables names. Though I did manage to get it to work for different table names in an alternative way. You could open the GUI, run the comparison and manually map the tables together, making sure the tick boxes are checked, then save the project file. Then you can call that project file in cmd. Though it's not what I wanted and it's probably the same for you. Annoyingly Redgate Documentation states "However, if there are schema differences between the data sources, for example if two tables have different names, they may not be mapped automatically." Kind of implies that they can be automatically mapped if the names are similar but this is not the case, one character difference at the end and it doesn't match anything. / comments
I'm looking for an answer too on this, I've had the same issue trying to run this tool in cmd for different tables names. Though I did manage to get it to work for different table names in an alter...