We have been seeing this as well. Customer will suddenly email us back saying the email sent had no content. When we check it has the thread but nothing that was typed in the response. I noticed that once the email starts dong this any attempt to reply will not allow you to type in the body as well.

Typically I have to convert the email to Text and delete the attachment for body.html and I can reply but it is messy as the thread format is lost and lots of HTML codes appear in the text body.

Very interested in someone figuring out why this happens. Thanks.

I have lots of samples if anyone is interested.