Do one of these:
A. If you want the formatting to still appear (e.g. **bold** for bold) then you need to keep the Markdown editor installed. You can have the plugin still there but set WYSIWYG as the editor to use for all new posts.
B. Update the "format" field in the "qa_posts" table - replace all occurrences of "markdown" with the format you want to use. Leave it blank for plain text, I think it is "wysiwyg" for the WYSIWYG editor but double check your database.
C. You could write your own script to convert the markdown in the content field to HTML and store that, then update the "format" like in B. (You can use the Markdown parser class that's in the Markdown plugin.)