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Hi Liz
If you are comparing encrypted and unencrypted objects enabling the WITH ENCRYPTION option should make unencrypted objects identical to the encrypted objects if there are no other differences in the object. I have tried this out and unfortunately haven't found the problem you describe. If it is possible can you email some example SQL to jonathan [dot] watts [at] red-gate [dot] com so we can take a deeper look into the problem.
Regards,
Jonathan
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Is there any way SQL compare can be set to ignore 'With Encryption' and just compare the objects themselves ?
Thanks
Liz