So, this happened a few weeks ago, and now it's happened again.
For reference: 2014 A5 sportback 2.0TDI (140)

First time was stop start not being able to cycle properly (car told me to manually restart the engine) causing the EML to come on.

Last night I drove almost 500 miles, Stopped off to grab a drink and have a rest, I got in car, pulled upto a stop sign at a services road, and as I didn't remember to disable stop start, the EML came on again. It usually stays on for a couple of days, then goes off on its own.

I'm going to book it in for later this week to have Audi have a looksee and see what they can find, but out of curiosity, what OBD readers would you guys recommend as if this keeps happening, I want to be able to see what's causing the issue and get into it as it happens.

Cheers!

My advice would be to get the battery tested to see if it's on its way out as batteries can cause electronic issues. 

In failing that you could get a diagnostic check carried out as the fault code will be stored on the ECU. 

Could be a dpf issue. But I'm guessing