I have a Yahoo mail account since 2001 and have kept my original messages on the server since then. As far as using an offline version of Thunderbird is concerned, I do not worry about my old pop3 messages as long as the most recent messages are listed towards the top (selectable by option).
The issue gets to be critical when I want to host an imap instance on my physical device inbox. The current count is about 120,000 messages, and is auto-downloaded every time I run the Thunderbird application. However, 120,000 messages is just a ball park figure, and I do not know the actual message count.
Looking at the Properties of the inbox, there is a message count approximation of about 100 messages more than the stated message count. Is there a way to "Get Messages" with the actual message count ?