Confrused -
You can use VB3 or VB4 (16-bit) to write apps that will run in the WinOS2 subsystem of Warp. OS/2 never added any Win32 support, so VB4 (32-bit), VB5, VB6, and VB.NET are out.
If you want to write a native OS/2 app to communicate with your Windows 2000 machine, the IBM Visual Age C/C++ is the way to go. The Borland compilers for OS/2 (of which I got suckered into buying both versions) were never that stable. The Gnu compiler is pretty good, but not that easy to set up a project, plus you'd need an editor.
How do you plan to communicate between the two machines? Warp has the ability to connect to Windows networks using the NetBEUI protocol, so you can share files. You could also write sockets programs on either side. I think (but am not sure) that named-pipes will work across platforms. Direct database access is probably out, as OS/2 never shipped with ODBC drivers (you can get a ODBC driver manager from Merant, I think, but you may have to find the one person in the company who knows about it).
Good luck on your project.
Chip H.