I have two account setup on the free version. I just registered and activated the trial sync feature and now one of my account folder structures is completely gone. I can still send/receive that account, I just cannot see the folders any longer.
I will assume you mean email folders tree (otherwise let me know). What email type do you use (POP3 or IMAP)? For POP3 you won’t see tree structure from the server. If it’s IMAP and you think you should see folder structure, we would appreciate if you send us logs: go to menu Tools->Settings->Logging and check IMAP (and be sure you use the most recent version of eM Client). Then restart eM Client, try to simulate the issue and send us the logs (with reference to this topic) using the same logging settings window.
One is an IMAP and the one that dissapeared is a POP3. How Do I revert everything back to the way it was so I can at least see my pop e-mail folders?
They are locally stored (at your disk) so it should be there (and activation shouldn’t change anything in it). If you cannot find them anywhere only option for you is to recreate you POP3 account again that will download emails again. But be aware about account setting (menu Tools->Accounts) in POP3 tab about storing messages at server after they are downloaded.