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Thanks for your post.
At what point during the comparison do you get the error, and what is the message?
When you compare a script folder to a live database, the comparison results will tell you which objects are missing, additional or different. If it finds an object that isn't in one of the schemas, it should report it as a schema difference, rather than throwing an error.
Did the script reader give you any parsing errors? -
You can get an error like this if you have a partial script folder which has objects that rely on a table (e.g. indexes, triggers, foreign keys) that don't have a corresponding table. SQL Compare only handles script folders with complete objects - incomplete objects will cause problems.
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So, how would I compare VSS version of the db to a partially complete instance in the SQL Instance?