Should I Be Worried about Tooth Pain 2 Weeks Post Interproximal Reduction for Invisalign?

Normally with IPR any sensitivity is immediate so it may very well be tooth movement.  It could be something else and an x-ray may be needed to see if the pain is coming from under the tooth such as a possible abscess.  Call your treating dentist or Orthodontist and have him check this out if it persists more then a couple days especially if this is several days into a new aligner and not the first day after a change.  Good luck!

Inter-Proximal Reduction (IPR) is a method of gaining space in order to re-align teeth.  This is sometimes done due to tooth size discrepancies or large amounts of crowding.  The IPR is always limited to be no more that a quarter to half a millimeter of enamel and should never extent beyond enamel.  Because only enamel is reduced there is almost never any discomfort following the IPR.  Fluoride can be used to re-mineralize the exposed enamel rods and make sure they remain cavity free.

If your tooth is sensitive is may be for many reasons, go back to your dentist, this may not be related to the IPR or perhaps a small amount of root surface was abraded leading to transient sensitivity.  Its best to get this checked out.
 

I am not sure how much IPR you had but normally it is limited to .5mm between teeth.  With that in mind your enamel is much thicker than that so you should not be experiencing any discomfort.  The teeth are moving and that could be what is causing your discomfort