When an ACMT (Apple Certified Macintosh Technician) working for an AASP (Apple Authorized Service Provider) performs an upgrade (the data doubler in this example) AppleCare remains fully intact except for the removed/replaced component, though it's assumed that the new component will have a separate warranty of it's own from it's manufacturer. However, when a non user installable part, such as an optical drive, is replaced by a non ACMT Apple has every right to assume the upgrade/repair was not performed properly since the person has not completed the training/tests Apple provides to ensure they know and follow Apple's repair guidelines. This is the instance where they can (and often will) deny warranty coverage. Typically though I wouldn't expect a Genius/AppleCare rep to even bring it up unless the failure is within the same area as the upgrade/repair.
Basically, if you can provide a receipt showing the repair/upgrade was performed by a recognized AASP then you have nothing to worry about. If you performed the upgrade yourself and it's in the same vicinity as the suspected failure then you might take the time to reinstall the original components.
edit:
Just to clarify, the only installable components that come to mind are the hard drive & RAM in MacBook Pros. All other components would be considered non-user replaceable by Apple/AppleCare.
Something to check too would be software. Try booting to a recovery disk or secondary OS and playing sound. I've seen corrupted software cause sound distortion several times. Probably still a hardware failure but one more quick check that could maybe save a trip to Apple.