Collectibles glitched in a specific save

I've had this issue in the same save for a few weeks now and have tried every possible fix listed online. I deleted the cache, removed all of my mods and custom content, and even repaired the game. I know it is specific to this save, which I've been building up for years, because I tested a new save, and collectibles are spawning just fine. It's not that they won't respawn after collecting them; rocks, crystals, and time capsules do not spawn at all, period. Has anyone found a fix that will work without starting over completely in a new save?