In MySQL&#x2F;MariaDB (and presumably other major databases) you can instruct any given query to ignore an index, but it has to be done at the query level.  Perhaps the db interaction layer of the application code could be written such that all select queries are built with a variable containing a list of indexes to disable.  You could then set that globally (or using dependency injection) and any query using the index would stop using it, without needing to go around and search for uses manually.