Right-click the account in the folder pane, Subscribe, click Refresh. Do the missing folders appear in the list to check, i.e. subscribe?

I don't have a Subscribe button to click on? I have seen this fix before but can't seem to figure this out.

Subscribe is only for IMAP accounts. Check the Server Type under Tools/Account Settings in the Server Settings section, at the top.

It shows as a POP mail server

POP accounts only download the Inbox, not custom folders or Sent. See this article for how to convert to IMAP:

https://support.mozilla.org/en-US/kb/switch-pop-imap-account

If I change to a IMAP will I be able to retrieve what I have lost or will it only allow me to do so going forward?

If you change to IMAP, you will see whatever folders that are visible when you access the account through webmail. As the article mentions, copy your current folders to Local Folders as a backup before removing the POP account.