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HiĀ DenisJCilliers,
What objects are you seeing this on please?
The setting in specifically for ignoring case differences in PL/SQL blocks as detailed here.
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It does not ignore case when the setting is enabled nor does it script out the case changes when the setting is not enabled.
Thus I have a Stored Procedure that is constantly found as changes to the database but the only difference is the case.
The workaround is to delete the current script file and let Flyway build it again from scratch based on the database version.