The Win32 kernel API function EncodePointer was added in Windows XP SP2 (client) and Windows Server 2003 SP1 (server). These are the absolute minimum versions of Windows that provide the requested functionality.
Hence, if the software you are trying to run needs it (which it sounds like; there would be no reason to map it otherwise), that software is not and can never be compatible with Windows 2000.
You may be able to get this software to run by upgrading to Windows XP SP2, assuming (which is quite a big assumption) that this is the only additional thing needed. The correct thing to do would be to contact the software vendor and determine what minimum version of Windows is supported by the software in question, then use at least that.