@TomJNowell I decided to "freshen up" my local development copy of the database from the production database. Exporting/DB Replace, etc. Two of the sites in the database didn't update with the DB replace script. So I went to see why... and poof. There's the problem. No indexes on those tables randomly.
I also tried Dashboard -> Updates -> Reinstall // Dashboard -> Updates -> Upgrade Network and that didn't fix it either.
I looked into the update files for WP core... They don't even verify DB integrity. Can you believe that? They offer a "reinstall" feature, but the reinstallation doesn't even check the database at all. lol
If you look at wp-admin/includes/schema.php will get you the schema via wp_get_db_schema(). I was thinking maybe something like dbDelta( wp_get_db_schema() ) ??? idk
Either that or I was thinking about building a custom class which specifically checks the database for indexes. If any are missing, it will readd them.
Think I'm SOL here tho. unfortunately. Lot of work to fix something stupid.
@TomJNowell Once upon a time though, these sites were all standalone installs. Migrated them all into multisite. They all functioned fine pre-migration and post-migration. So I'm not sure how the indexes disappeared.
