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Hi @twurm
We do have the option to "Ignore Indexes", however, this will ignore all indexes within the database.
https://documentation.red-gate.com/sc/setting-up-the-comparison/setting-project-options#Settingprojectoptions-Ignoreindexes
Unfortunately, we don't have a way to filter indexes individually as they're a part of the table, and using the above option would essentially be an "all or nothing" option.
If you wish for indexes to be filtered, then I'd suggest making a post on the UserVoice here which is used to plan new features: https://redgate.uservoice.com/forums/141379-sql-compare
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The problem is next time we upgrade their instance we wipe out the index via SQL Change Automation and Octopus Deploy. An example index name is below. We name all of our indexes IX_% or UX_% so even a filter that we could specify would help.
nci_wi_OrderReleases_6457001BFC842C960F78B76AAF900533