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Can I ask which version of SQL Source Control you're using? There were some fixes in version 6.0.0 around handling DISABLEd indexes (issues SC-9520 and SOC-8863: https://documentation.red-gate.com/soc6/release-notes-and-other-versions/sql-source-control-6-0-release-notes)
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I am using version 6.0.8.7147.
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I've reproduced the issue here, and recorded a bug with reference SOC-9337.
There is a workaround you can use though - if you delete the relevant `ALTER INDEX ... DISABLE` lines from the files in your version control system, commit the change (using the version control system's interface), and then do a Get Latest, the difference should disappear. Exactly how you do this depends on which version control system integration you're using - if you need help with that, can you tell me which system you're using and I'll give you more specific instructions.
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Something to note is that all the objects are tables, and the changes to the tables are removing an "ALTER INDEX" statement from the script: