I did just a quick test and didn't keep the changed files.
But here's a quickly made DAXBuilder tool with a GUI that might help:http://personal.inet.fi/koti/jhirvonen/gbc/daxbuilder.zip
It needs to be put in the same folder as Gold Box Companion as it needs some of the data files from it.
Run it, set game folder / select the game and the DAX-file. Extract the DAX contents and then open the ECL1_021.bin from the extact-folder with a hex editor.
Starting roughly at hex offset F60 and onwards there are several sequential byte runs of 34/32/36 etc. which some of probably are the encounter contents.
So probably not all encounters are created with the 0B command but use lists / tables.
After hex editing, rebuild the DAX with DAXBuilder. Of course, the game must be reloaded after changes. It's probably best to restart DOSBox as well.
That's all I know. I can't point you at exact offsets to change as the format of the ECL files is not completely understood.
Also, try using Gold Box Explorer to figure out the ECL file structure.