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Hello Elsie,
Unfortunately there is little I can suggest. The whole idea is that SQL Data Compare needs to compare all of the selected tables' contents before it can generate a synchronization script, even if the amount of data eventually being synchronized is very small.
It is possible to cut down the amount of data by specifying a WHERE clause on the table. This can be done in the user-interface version of data compare only, so if you wanted to utilize this for the command-line version, you would need to specify a WHERE clause in the UI version, save the project, and use the /pr argument to Data Compare to load and use this project.
I hope this helps you.
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Please let me know if you need any additional information.
Thank you.