This is a tough decision, in my opinion. I've sold and traded plenty of cards over the years to add cards to whatever was my 'core focus' at the time. Never have I considered selling/trading something *in* my 'core collection' to add something to that very collection.
If I was faced with that decision it'd probably boil down to which group of cards I'd rather own -- those that I wish to obtain or those that I would have to give up to obtain them?
And in terms of giving up some tough cards, which card or cards am I more likely to have a chance to obtain again -- those that I wish to obtain or those that I would have to give up to obtain them?
Gut feel just based on how I read your initial question, those that you could obtain are more difficult, and although tough, those that you have are more likely to be re-obtained. Based on that, I say go for it
And on that note, something else you might consider: Perhaps those that buy the cards you sell are willing to give you the 'right to first refusal' if they ever decide to sell/trade those cards away.
Good luck, which ever way you decide to go.
Richard.