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You can get all the command-line help by running the command-line with the verbose and question-mark arguments: there is a lot more there than what you find on the help pages of the website.
sqlcompare /? /v | more
To specify a transaction isolation level, use transactionIsolationLevel, or tilsqlcompare /til:SERIALIZABLE sqlcompare /til:"READ COMMITTED" ...
Hope this helps.
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http://www.red-gate.com/supportcenter/C ... v10#o14908
How do I set this option from the command line when running SQL Compare from a deploy script?