I am trying load a save from the other day using the exact same mods but this time it's saying there is a mismatched error and I can't load the mods anymore. I have looked for solutions but most use the apply button which I seem to no longer have as of today.

You don't seem to need to apply anymore, just select the mod and it auto applies. However, this update broke a lot of mods, make sure the mods you're using are updated for Bonny.