Enabling downloaded mods after Integrity File reset?

[kitakeetz]

After realizing my backup failed I had to do an "integrity check" on steam for Stardew Valley. I also re-installed smapi, and all downloaded mods show up in the promp screen. But when I load the game none of the mods show up at all. I'm not sure what I'm doing wrong? Redownloading some of the mods isn't working either.