It will affect it to some degree. How it affects it would depend on how much material is removed and where on the core it was removed.
Like drilling into the pin, your drilling into the tallest part of the core. This in effect would shorten the core reducing flare.
Your getting into a real technical aspect of drilling and For the majority of normal drillings. It's not something you really have worry about.
Of coarse dont drill holes any deeper than you need too.
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