On the whole, it is better to fix things in the BK9’s sequencer than in the make up tools if you are planning on using an external player.

There is some weirdness going on with the sysex and the way the makeup tools address the parts. I’ve never really tracked it down too carefully, because I only use the BK9 to play my Files, so everything works out. But on the whole, ‘freeze’ only goes so far, it can’t translate everything that the make up tools is doing into regular MIDI.

But if you make your corrections to the sounds each part addresses with the sequencer, the file plays fine on anything. A lot depends on how deeply you are using the make up tools, as there are some very deep drum kit editing possibilities there, plus EQ and MFX Changes you can make that really need a ton of sysex to express.

However, it strikes me that there is a workaround you might try… Each performance can be called up with a MIDI code. Perhaps if you get the external player to send the code that calls up the performance, it might be worth checking if the part now plays the correct sound.
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An arranger is just a tool. What matters is what you build with it..!