Note for Apollo Thunderbolt users on Mac OS X: The Apollo I/O can be manually changed on the Core Audio tab of the Console settings. Repeat these steps for the 'Output', 'Bus' and 'Insert' tabs as well.
This will re-populate the tab with the correct paths. Delete all paths on this tab so it is completely empty. To do this, open Pro Tools and navigate to Setup > Playback Engine and make sure 'Universal Audio Apollo' is selected.
Follow the process below to reset your Pro Tools I/O. Pro Tools' I/O settings can get changed for a number of reasons and it is sometimes necessary to reset the Pro Tools I/O to resolve issues with routing audio in to and out of Pro Tools.