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Response from RedGate: "placed it into the bug database for the Red Gate development team placed as SC-3890".
Thanks guys! -
Just to clarify this point a little:
There is a bug in SQL Compare where if the synchronisation process involves dropping an index, the index will be dropped; regardless of whether or not the Ignore Indexes option has been turned on.
Unfortunately SQL Compare doesn't yet work out which situations are safe to retain the index, but hopefully this issue will be looked at for a future release.
Alice Easey
Red Gate Software
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(SQL Compare 6.2.0.271)