As long as you keep the emotes there, they'll stay. However, if you have not streamed for...I think it was 60? unique days as an Affiliate within 2 years or something like that, you don't qualify for auto emote uploads and won't allow you to reupload channel (not sub) emotes after you delete them.

That's dumb and messed up. Hope you're able to get that quota filled soon so you can play with the emotes!