It's interesting I've never run into this problem and I do a LOT of copying of presets. However I always export then import them, then make changes and export them to a new preset name. Maybe this relates to an "in memory" copy of the presets?
Like @enjaltsuggested Command Center's Preset Command does what you want on the Stomp itself. So if you program a footswitch to reselect itselft you can then externally trigger that footswitch with MIDI CC#48+X where X is the footswitch number. A bit clunky but it works.
When in Edit mode, long press the "Exit" footswitch to save the preset. I should actually say so in the scribble strip display too, at least on the Helix Floor.
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