It is not recommended to use any on board sound card with Sonar. But of course it will play back audio if your willing to do a bunch or re-configuration of your audio. If I disconnect my USB interface from my laptop, the wave files are all still there and they all look just fine, but, I would have to go into Sonars Audio preferences and change the whole shebang to my on boards MME driver etc , and change my master buss et before anything will play again. So I don't ever do this. Reason being, Sonar hates it and will cause me grief the next time I go to record using my proper ASIO interface.
Just leave the Line 6 hooked up. Sonar will be happy and you will have no problems, unless the line 6 has crappie asio drivers or whatever.
Before you record next time, make sure the tracks input is set to the line 6 and that the meters are showing a signal.