This message is not to ask "what is the problem exactly" but to suggest a solution. Maybe what I'm about to write is dumb and has nothing to do with the issue, but here goes nothing. I've done that successfully in some pseudo-VM I was writing in AGS :
Split the pointers address range in two. I mean, a pair of completely artificial "fake" addresses ranges. For example :
0x0000 --> 0xFFFF = old-style pointers, nothing changed.
0x10000 --> 0x1FFFF = managed objects. You generate those exactly like you used to (values from 0x0000 to 0xFFFF), but you immediately add 0x10000 for as long as they're passed around as value from C++ function to C++ function-
With a simple binary mask you can tell which value represents which type. <= 0xFFFF = regular pointer. >=0x10000 = managed pointer.
Whenever you need to actually read/write to memory, just remove the bogus offset : For example, convert managed pointer 0x100AA to 00AA, then do whatever you would normally do (pointers arithmetic, real address in memory, etc.)
Food for thought.