A bit complicated, but to explain;
 
* Recording acoustic guitar from both pick up and mic, on separate tracks simultaneously, using Focusrite 2i4 into Sonar Professional (W10. ASIO)
 
* Plug pickup into Focusrite left input, set track input in Sonar to 'left Focusrite USB 2.0'
 
* Plug mic into Focusrite right input, set track input to 'right Focusrite USB 2.0'
 
* Record both signals on separate tracks, no problem
 
Problem - if I turn off PC at the end of the day and power up next morning, I get no sound from the Focusrite, in or out.
 
Workaround -
 
* Arm track inside Sonar and set track input to 'stereo Focusrite USB 2.0.'
 
* Restart PC.
 
* Sound is back.
 
This problems ONLY occurs if I use both inputs on the Focusrite simultaneously, otherwise the sound is there after PC is restarted next day.
 
Hope I'm explaining this clearly. Any clue as to what I'm doing wrong, or missing here?

I would be talking to Focusrite support (there in the UK).  I doubt that its a Windows problem.

I just did. They think it may be because my PC is set to 'fast start up' and the 2i4 isn't being recognised on boot. I get sound back if I restart, because fast start up doesn't affect that, so best guess is that restart gives the PC time to 'see' the 2i4.

You can disable fast start up.  I did that on my system.
 
Here is the instructions from the Win 10 forum (tenforums.com).
 
http://www.tenforums.com/...indows-10-a.html?ltr=F

I wonder if stopping and restarting Windows Audio in services.msc would reestablish audio. It is faster than restarting and might be scripted.

Maybe this is related?
 
http://forum.cakewalk.com/How-I-solved-my-SonarScarlett-Windows-freeze-problem-m3324002.aspx
 

It might be but the differences might suggest otherwise
The Focusrite 2i4 Bus powered
Different OS
The symptoms are not the same
 

scook
It might be but the differences might suggest otherwise
The Focusrite 2i4 Bus powered
Different OS
The symptoms are not the same
 

Yeah, I just realized the workaround can't be tried here (since its bus-powered).

Thanks guys. The 'fast start-up' seems the most likely culprit, and I see how to disable that. It's odd though, that this has only happened the 3 times I've done that dual input recording on the 2i4. Been fine every day since I got it otherwise.

Let us know if disabling the fast start up it fixes it.
 
With fast startup enabled, Windows cache's some items and its similar (not exactly the same) as Hibernate.  The faster startup, for most, is not a big deal.