When I open a patch including poly~ objects, the encapsulated patcher (still in Max4) is not found, so all connections to and from poly~‘s instances are removed. And they are lost once I save the patch in Max6. This is quite annoying!
The same thing happens with Max4 abstractions.
Fortunately, this is not the case with Max5. So I first need to open the file in Max5, save it as a .maxpatch file, then open it in Max6.