How to recalculate connections/airwires from copied traces?
If you have simply grouped and then copied them, you will have to make sure that the pad names on your IC package are the same as the wires you've connected to them. 

I just did a little experiment to see if that is correct and it is, you need to rename the routes to match that of the pad - hole connection (you can do this by using the 'name' tool and clicking on the yellow, 'unrouted' connection showing you where the connection needs to made. Once you know the name, use the name tool and rename the tracks that you wish them to be connecting to. You may have to do a little connection on the pad because Eagle won't think it's completely connected but it will show up with the thin yellow lines again if this is the case.

One last thing, did you use the 'route' tool or the 'wire' tool? Route is the correct one to use as it will continue to show you the 'unrouted' connections while you are making them.