"Tools/Global/Adjust Minimum Attenuation" seems to ask for a number. Then it changes the attenuation of all instruments equally, ensuring that the minimum attenuation is equal to the selected value.
The problem here is that it assumes that empty fields are 0db attenuation, and fills them out with delta-attenuation. This is incorrect, as they actually inherit instrument-global attenuation. Let's say 20db of global attenuation, delta = 10db. The proper value is 30 db, but Polyphone fills out 10db.
The solution is to leave empty fields blank (inherit), except for instrument-global attenuation (you should move "starts-from-zero" from instrument splits to instrument-global).
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Also can you add a feature for "attenuate entire soundfont by fixed amount", instead of "minimum attenuation"?