If you lost the POP folders, you would need to have backups to restore. Maybe I'm not understanding, but you cannot restore what has been lost. Maybe more information will prove useful.

You can't change from POP to IMAP by just changing the settings. The account has to be added as an existing account with IMAP settings.

http://kb.mozillazine.org/Convert_a_POP_account_to_a_IMAP_account

My folders are in C:\Users\Owner\AppData\Roaming\Thunderbird\Profiles\94cv9wue.default-release\Mail\pop.cox.net. How can I restore them to my new IMAP account?

I will assume they are in your current profile. If not, with Thunderbird not running, you can copy the message folders to the Mail\Local Folders folder in active profile. From your post, I infer you are comfortable with that task. If not, just ask. Now, uploading messages to IMAP is NOT a strength of IMAP. If only a few messages, just highlight and move them with context menu. Ifa lot of messages, I encourage creating a filter to manually COPY them, as that regulates somewhat the transfer. After success, you can then delete the local message folders. Do NOT use MOVE, just COPY (to protect you in case the transfer to IMAP causes corrupted messages).