If this is the case, temporarily disable them and check if messages arrive in your Inbox folder.

Make sure there are no mail filters that delete incoming messages or move them to other folders. This is a filter that deletes or moves email messages You can delete messages from the client, but leave them in Yandex.Mail by configure the client using POP3, but we don't recommend this as messages might not sync correctly with the server. Now restart Thunderbird and it will automatically prompt you to enter the password.

Open ‘Tools’ > Preferences > Edit Preferences > Go to ‘Security’ > ‘Passwords’ > ‘Saved Passwords’ > Click the account and then click ‘Remove’. This is because your client uses the IMAP protocol, and the inbox in your client is synced with the service. If that’s the case, you need to update it on Thunderbird as well so it can connect with the servers without issues. If you use an email client and delete email in it, messages are removed from the service page as well. The configuration process is easy: you just need to. You should also make sure there aren't any unknown phone numbers on the Phone numbers page. Like any other mail client, also Mozilla Thunderbird needs an outgoing mail server to work correctly. If you are sure that only you have access to your mailbox, test your computer with an antivirus software, change the password and alternative address. If more than 2000 actions were performed after the messages were deleted, data on the delete operation will not be displayed in the log.

Mozilla thunderbird email problems