I am using SW2014 SP5.
Inserting a part in a part always strips the hole wizard intelligence. This happens whether you insert a part in part, or save out the part with Save Bodies, Insert Into New Part, or Mirror Part.
It is a cause for a significant amount of non-value-added work in SW.
If you want your drawing hole callout's to be parametric again, you can fill the holes in your new part and then recreate them with hole wizard using the hole fill sketch as a location reference. For the hole fill sketch I usually just convert entities selecting the hole edges.
Why do I fill the holes first? Even though you will be putting the same size hole back in about half the time - probably due to the rounding algorithm - SW will fail the new hole because it is "smaller" than the dumb hole you are trying to over write. Your option is to either make a custom hole size for your new hole and increase it by a few thousandths so that it is actually "cutting" new material or fill the hole and use a standard hole size. For me, always filling and drilling is less wasted effort and consistent instead of playing the lottery and hoping this one wont fail.
Is this a PITA? Absolutely. A waste of time? "It Depends". My biggest driver is that I want to be able to use Pattern Driven Patterns. Unless you reestablish the hole pattern, the Pattern Driven Pattern will not recognize your holes from your stock body. And I want to use the hole callout tool in drawings as well.
If any one else has an easier work around I am ALL EARS.