The add-on content is just the official update files, so boot up your 3ds/2ds
3DS system settings --> Data Management --> Nintendo 3DS --> Add-on Content
Then just delete the relevant game's data. You can re-download it at any point.
Make sure you'v deleted the add-on content for the game you're trying to patch my guy! Had the same problem with sinking sapphire awhile back and that seemed to work