Hi Zeoilam, This phrase sounds unnatural, as "bother" means someone or something that causes continual and minor irritation. Since you are sending one email, it does not cause continual annoyance. You can indicate your goodwill by writing this instead: "I hope this email finds you well." In this way, you wish that things are happening well for your receiver.

Because you sent the email so late - as you stated in your reply to Mr. Lance - I think your best reply would be, "I hope this email does not disturb you". To bother someone is to annoy or pester them. To disturb someone is to interrupt them from something. So, in this case, you are basically expressing that you hope you are not interrupting them from their sleep, or rest.