Accidentally Sent accessories with my controller for repair, will I get them back?

There's no guarantee they will be sent back.

I was recently sent an email with a note that said " If you sent any additional accessories with your non-functioning device, they will be returned to you in a separate shipment" Is this just an automated message or does this mean I will get them back, if so, how long will it take to receive them?

There's no guarantee they will be sent back.

You can request a call back or chat with support at http://support.xbox.com/contact-us If you're not seeing those options, change your category/topic until you do. Billing & Subscriptions and "I don't recognize a charge" usually works for me.

Unfortunately, the support person you originally spoke to did give incorrect information. Hopefully support can rectify it, but there is no guarantee they will ship anything back that was sent in.

That is very odd as you are not supposed to send anything except for the console when you schedule a repair. The console gets sent back without the controller or cables and people usually need to make a special request in order to get their cables or controllers
sent back to them after the fact.

the warranty is typically 90 days in the states for accessories and 90 days from the day you receive your controller back from the repair center.

Try and contact support again and see if they will be able to create another repair order for you to send your controller back into them.