If I'm reading my galvanic series chart
(see link) correctly copper your copper flashing has potential
to eat away zinc (galvanization) and iron (the body of the nails). This is more of an issue when the metals are wet (hopefully they won't be under the flashing). If the nail heads were corroded away the shingles would be more susceptible to blow-off... but at least they won't be eating holes in your flashing!
My comments are strictly theoretical, as I have no experience with the combination you are talking about. My guess is that it will be fine, but you could always put a dab of sealant on the nail-heads, or a layer of 15# felt between them and the flashing if it makes you sleep better.
Hopefully a real roofer will chime in with some more experienced advice.