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Hi delapohl
It looks like something has gone awry with the mappings. Are the 16 tables all part of the same schema? If so you may need to check the owner mappings - https://documentation.red-gate.com/display/SC13/Mapping+owners - and ensure that they are mapped correctly.
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Thanks Rob, that pointed me in the right direction. I had manual mappings for these tables from a previous release. I restored the default mappings for those tables, and that resolved the issue.
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When I compare two similar databases, 16 tables are showing up as "only in" both the source and the target. All of these tables actually exist on both the source and target. If I run the same comparison while running SQL Compare as Administrator, this issue does not occur. Another user at our shop tried it with his copy of SQL Compare, and he also does not see this issue.
Is there some metadata associated with my user that I can delete to resolve this issue?