Since today or yesterday, my Thunderbird has stopped refreshing the list of messages. The number of new/unread messages in the Inbox and other folders is shown and updated right but the main window with the list of the messages does not get refreshed and only shows the last message from couple days ago.

Did you activate the Quick Filter toolbar by inadvertance?

I've tried to follow a bunch of guides and ideas (repairing folder, deleting .msf files...) and even removed the account and tried adding it again. The list of folders is right but now there are no messages at all. All folders look empty.

Can you see the messages of this account when you open webmail?

I've found out that in the folder on the disc where there are supposed to be the "INBOX.msf" and "INBOX" files, that the "INBOX" file without the file type is missing. And it's the same with every message folder, there are only .msf files on my PC where I removed and re-added the account.

This is normal if you disabled ⬜︎ "Keep messages in all folders for this account on this computer" in Account settings > Synchronisation & Storage > Message Synchronising (see images) By default this option is activated.

Does the same issue persist if you start Thunderbird in "troubleshoot mode"? https://support.mozilla.org/en-US/kb/troubleshoot-mode-thunderbird

@Mapenzi: Turns out it was my e-mail provider fault. They made some update that blocked all their customers from Thunderbird. Now I got message from their support that the issue is fixed and my messages are back. However they didn't tell me what the issue was.

Thank you for your response and effort though. Still to answer your questions, yes, I did check all the points you mentioned; no quick filter, messages were visible on the webmail, folders had checked "Keep messages" and the issue was there even in troubleshoot mode.

Thanks for your feedback!