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Thunderbird does not provide a way of changing the POP3 timeout in the GUI. You need to create a user preference override.
You can do this by creating (or adding to) a file called user.js in your Thunderbird profile folder.
To change the POP3 timeout add the lines:
// Increase pop3 timeout:
user_pref("mail.pop3_response_timeout", 90);
In this example the timeout is set to 90 seconds (instead of the default 45 seconds of Thunderbird). Adjust the time as you need.