I've been using Inventor for about 6 years now and this positively drives me insane. Has anyone (cough...Autodesk) come up with a solution for this issue? You can go in and re-dimension your sketches, but more often than not, you end dimensioning to something you really don't want to just to get rid of an error that shouldn't be there in the first place.
I don't think you will get an answer from Autodesk any time soon. What you should do in a mean time is to avoid projecting model geometry in iParts. Project sketch geometry instead. Some times it is feasible to create a Shared Sketch and use it to control the features you need.
Here is a modified part for you.
Thank you for your help Igor. But really, Autodesk should be embarrassed by forcing users to not use model geometry as references in i-parts. If only some other software company had already figured out that suppressed features should also suppress the associated sketch.