I have an Octavia Scout and Smartlink was installed by the dealer. At the start Android Auto worked really well, more recently it does not connect to my phone and when it does the connection will drop after 5 minutes or so. Having recently had a rental car with SmartLink my phone worked perfectly and Android Auto worked a dream, back to my Skoda same phone same cable not connecting. Anybody had a similar problem and know of a fix? 

Did you try hard resetting the unit by long pressing the power button?

 

Also, I think Android Auto partially uses Bluetooth, so I would try to delete the pairing/profile and do it again, while answering yes to all prompts for access in the phone on the same process.