About the link you posted, I quoted some information:
Thunderbird : FAQs : Anti-virus Software
Email messages that you download using Thunderbird are not stored as individual messages on your computer but are instead appended to your Inbox, a single mail file found in your profile folder. (Messages can also be filtered to other folders or sent automatically to the Junk folder.) This means that when your anti-virus software detects an infected message during download, the actions taken by your anti-virus software will likely affect your entire Inbox. For instance, if your anti-virus software is set to automatically delete infected messages or files, this may result in your entire Inbox being deleted.
This is why I can’t say it’s an avast problem but Thunderbird one…
With this in mind, below are some tips for using Thunderbird with anti-virus software:
Make sure that your anti-virus software is set to quarantine infected files rather than to automatically delete them.
You can set the providers on Advanced tab to ‘Silent Mode’ and answer ‘No’. This will send the file to Chest, automatically 
Keep your Inbox relatively empty, or at least don’t store the bulk of your email in the Inbox. Instead, store most of your old messages in other folders. That way, if your anti-virus software ever happens to delete or damage your Inbox, few of your stored messages will be affected.
Set your POP3 mail account to leave messages on the server for a certain period of time (such as 3 days) rather than deleting them immediately when downloaded. That way, if your anti-virus software ever happens to delete your Inbox, you will then be able to download those messages that are still on the server. To do this, go to Tools → Account Settings → Server Settings, check the box for “Leave messages on server” and set the number of days. (Note: in some cases, setting Thunderbird to leave messages on the server may cause the same messages to be downloaded again and again. You will need to test your mail server to see how it responds.)
Good ideas or not, depend on your way of work, what is your technical level, etc.
Consider using third-party software such as Mailwasher so that before you download your mail into Thunderbird, you can scan the headers and delete suspicious messages from the server.
You can’t undelete these messages too…
Recovering a quarantined Inbox
- Switch off the “auto-protect” feature on your anti-virus software, or otherwise deactivate your anti-virus software; take the Inbox (or other affected mail file) out of quarantine.
- In Thunderbird, delete the infected message.
- Empty the Trash for the affected account.
- Compact folders for the affected account.
- Reactivate your anti-virus software.
Before going through the above steps, you might first want to make a temporary backup copy of the infected mail file or your entire profile. After you’ve successfully restored the Inbox, delete the backup from your computer.
Another suggestions and the way of Thunderbird works…