In the previous version of Toad there was an option called "Save ALL settings to a file" to run the comparison from the command line later, but the option is missing. Has it been moved?
The 'Save ALL Settings to a File' button has been removed in the Schema Compare tool. Saving settings to a file and then passing the filename through the command line is no longer supported and no enhancement requests will be accepted to bring the option back.
The option is available in Toad 9.6.1 or below, but it is no longer supported by Support.
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