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Thanks for your post.
You should be able to accomplish this by editing the project and going to the 'Tables & Views' tab.
On this screen you can select the custom comparison keys that you wish to use for the purposes of the comparison. Click in the comparison key field for the object that you wish pick your own comparison key, then change the comparison key to 'custom' and tick the column you wish to use for the comparison.
Also, if you only wish to sync a particular column, you can select/deselect the other columns in the comparison in the 'Columns In Comparison' field on the right-hand side. The columns that are selecting in this grid are reflected in the comparison and in the synchronisation.
I hope this is what you were looking to achieve.
Let me know if you need any more information.
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I'm using v5.0