In Thunderbird's menu, all open emails are listed in the tab bar. This is except for emails opened from your PC (or NAS server) as saved .eml files. A new Thunderbird instance is opened in Windows for these.
You can close open emails in the tab bar by clicking the x next to their names in the tab bar. EML files opened from your PC must be closed as a Windows app in the top right corner.
If you have multiple emails open—some by clicking on an incoming email, for example, or by opening related saved emails (.eml)—and you want to close one, you have to click the x in the tab bar for one email and the x in the top right corner of the screen for another. This results in you repeatedly clicking the wrong x, and Thunderbird closes.
Why aren't saved .eml files simply opened within Thunderbird and placed in the tab bar? This prevents Thunderbird from frequently closing accidentally. And, for example, if you're asked if you want to save changes and you say no, any open drafts will also be deleted.
So, please standardize the user interface.
Either: Open all emails as a new instance of thunderbird.
Or: Open all emails and put them in the tab bar.