If you modify the text when you're in the converted state, and click MarkdownHere button to convert back to original text again, you will risk losing some or even all of your text!
If you enabled HTML source editor mode and click MarkdownHere button in HTML source editor window, you will risk losing all your input text.
If you save the draft message and open it again for further editing, MarkdownHere may convert the text into wrong format of quoted block, because Thunderbird will beautify the HTML code with indention and MarkdownHere can't handle it correctly.
Solution: The HTML text should be converted back to plain text, before formatting them with Markdown. You can do it manually by copying the text, then Ctrl+Shift+V to paste plain text, then click MarkdownHere button to format them.
There should be a transform status feedback, when switching on and off of Markdown conversion. eg, MarkdownHere button pressed down or released up.
Conversion done by MarkdownHere is NOT recorded in Thunderbird undo history, so you can NOT revert it by pressing Ctrl+Z to undo the edit! This will cause data loss if you're not cautious when using MarkdownHere.