Do I get this right? You have two accounts X and Y and you have set reply to X in both accounts. That's nothing odd even if you have it at the same host. (I have three)

When it bounce do you get any explanation or error code?

Thank you for replying, turns out the problem wasn't one with thunderbird at all.

I have one account and have created a second identity within the same account, perhaps we mean the same thing, so I have the original: JBlogs@example.net, and then a second email, JosephBlogs@example.net. It should reply to either to the JBlogs one.

It didn't because the email server blocks unauthorised @example.net addresses, as spam.