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Thanks for your question. If memory serves, SQL Data Compare refreshes the schema and then "replays" the mapping actions that you went through in the user interface. If there is a change in the schema of the table or view, however, I believe this renders the mappings null and void, and you are left with the "default" automatically-generated mapping for that object.
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I have went through my databases and created all the custom mappings between the two servers and saved them. However when I re-open the projects a majority (2/3) of the custom settings are no longer present... Can someone please help me with this?