Generally these sort of issue are caused by Antivirus programs timing out the server side updates because they are just slow in doing their thing. A silent failure Other things that can be implicated are. Outlook overloading their servers and not making updates as they say they will in a timely manner. Some years ago Hotmail moved deleted mail to a POP deleted folder, but they failed to do it sometimes for days and the result was the same mail reappearing in Thunderbird. Some folk think their mail client is on some sort of instantaneous server connection and have it checking mail every few minutes. This can lead to outlook simple dropping connection attempts. This is bad is the mail client is trying to delete messages using the connection. On a similar line, outlook limits the total connections to their server for an account to I think 5. Thunderbird will try and use those, but sometime a tablet and a phone will also be using connections, so things just slow down.

The fact you say 10,000+ emails sounds like you might be attempting to do a major house cleaning. Exactly how are you deleting these mails? (generally deleted messages go to the trash folder. Are you saying they never get there?

Also, when deleting so many messages that you know you do not want and will not want to recover, use shift+delete which will do an immediate and unrecoverable delete.