Secondary email says I'm out of space but I'm not.

Jonothon wrote:

Like I said, i've been using the secondary account to login for many years, what happened?

Dropbox has never ever worked like this I'm afraid. Secondary emails are simply for getting shared emails etc. They do not allow you to log on with 2 diff emails to 1 account. So its worked fine until something has pushed you over quota. 

To solve it check what data you have on both accounts - as my guess is that its different.

Go to the one which is paid and change that email to a one you dont need/use (its just temporary). Then go to the free one and use the email from the account you just released the email off (i.e. the one that's paid) as a swap. You can then go back to the paid account and change the email to the one you want to use. 

The only to then check is that the data on both is correct - so move things around if needed.