The IrPanels program lets you paste in a single block of text containing many Pronto Hex strings and it creates a CCF file for the whole set, which you could then merge into your working CCF file.

IrPanels is very limited in its input and output formats, so it might not be what you want (in which case I don't have a better suggestion, sorry.).

My MakeHex program was designed to produce as output the format IrPanels expects as input, so you might want to look at that as an example of how to make input for IrPanels (or write your protocol as a .irp file for MakeHex and skip the Excel part).