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Simple change to stored proc causes almost all foreign keys / indexes to be dropped and recreated

I have been struggling with this problem for weeks.  Our sql deploy will work just fine if there are no changes between the source / target (script is empty).  If I add so much as a comment to a stored procedure; almost all of our foreign keys, indexes, triggers are dropped, the stored proc is updated, and then the indexes, keys, triggers are recreated. 

I cannot for the life of me understand how a comment to a stored procedure would have all of these dependencies.  I have been over the redgate source control options, along with the sql compare options and I nothing seems to jump out at me.  I have tried the following options:  

And excluded some of the tables that I thought might be causing the issue.

It seems that this causes "less" indexes and keys to be dropped, but then I get fk constraint errors in our deployment.

I'm at my wits end on how to solve this; has anyone ever encountered this?  

Thank you!

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