This sounds like you use an imap mail account. IMAP mail accounts keep all emails on the server. In Thunderbird you see a remote view of those folders and emails. When you delete an email from the server via webmail using a browser or via phone, then Thunderbird will not be able to see it because you have deleted it off the server. Equally, if you delete an email via Thunderbird, it will be removed from server. So in effect, you have different ways of accessing the same folders held on the server.

It would be usual common practise to periodically create backups, so that there is more than just one copy regardless of whether emails are stored on server or on your computer. If you have a backup then now would be the time to use it to put emails back into the imap mail account and thus back onto server.

If you have a gmail account, then they archive everything in the 'All Mail' folder, so you may be able to check out that 'All Mail' folder and get them back into respective folders.