Yes, as long as they have different addresses. You can even lash them up, but you have remember which is which during the setup. I ended up with three ATSF GP35's with the same road number (I quickly changed two of them using Microscale decals). They all had different addresses in the remote and I edited the engine names later.
One issue that might come up is if the engine(s) were tested and have the same address. That happened to me on a recent purchase. The solution there is to edit the address of the first one, then add the second one.
