General > Protocol Configuration in PBConfig defines the protocols a caller can choose. The definitions live in PROTOCOL.PRO.
Because callers connect over TCP/IP, the board can use the standard built-in protocols:
The PBTerm terminal program supports Xmodem, Ymodem, Ymodem-G and Zmodem for the caller's side. See PBTerm.
Your 16-bit PROTOCOL.PRO is converted when you upgrade. Use the built-in protocols rather than 16-bit DOS protocol drivers. See Upgrading from 16-bit ProBoard.