At the Enter password prompt, you enter the special app password, but do you select the checkbox 'Remember Password' so that password manager saves it ?

If no then this explains why it is not saved. At the next password prompt enter password and select the checkbox to remember password.

If yes, you do select checkbox to remember password please then check to see if it really is saved in Thunderbird?

• Settings > Privacy & Security
• Passwords section
• click on 'Saved Passwords'
• click on 'Show Passwords'

Do you see the account - there should be at least two lines one for incoming and one for outgoing and is the Password the correct special app password.

If yes, it is being saved, so why has this gone when you next start Thunderbird ? Check for programs on your computer which clean up files such as session, temp or password. eg: CCleaner or WiseCleaner or some Anti-virus products If you use these products then I would advise that you make your Thunderbird profile exempt from scanning. They are known to be a nuisance when it comes to deleting files that are required in Thunderbird.

At the Enter password prompt, I enter the special app password and select the checkbox 'Remember Password' so that password manager saves it. In the password there is only one lines for incoming, none for outgoing, why?

When you send an email it should ask for password so do exactly the same - enter the special app password and select the checkbox 'Remember Password' and then check to see if password for smtp://account has been saved.