iCloud Storage Issues...

I've recently purchased an extra 50GB of storage on my MacBook Air, though I'm still receiving "disk almost full" messages, telling me to clear up space. I've checked, and I still have 46GB left. Still, I've tried clearing out my documents by putting them onto an external flash drive. I've deleted photos, emptied folders, but nothing seems to work. I've restarted my computer, but every so often I'll still receive the "disk almost full" pop-up, and it's driving me crazy. Anyone know how to fix this?