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Invoke the command line (assuming you have the pro version of SQL Compare).
Loop through your database target names using these switches:
sqlcompare.exe /s1:yoursourceserver /db1:yoursourcedatabase /s2:yourtargetdb /db2:yourtargetdb /reporttype:Interactive /report:yourreport.html /force
There are a number of different report types you can try. More info here:
http://www.red-gate.com/supportcenter/c ... _in_the_cl
David Atkinson
Red Gate
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Thanks for any info.