I assume you generated a full set of commands with MakeHex, including commands that you already have by learning and additional commands that you hope will include discretes.

The MakeHex version of the commands you already have from learning ought to work at least as well as the original learned commands. If they don't, then you did something wrong in the process of generating or importing them.

You can decode some learned commands (with DecodeCCF or the JP1 version of IrTool) to find the exact protocol, device and function number. So you can know exactly which MakeHex command corresponds to that learned command.