Hi, I'm absolutely shocking with MIDI, but it sounds like a patch call is being sent out by cubase at the beginning of the loop, and therefore it reverts the patch preset to its original saved state each and every time it loops.
An option would be to have all of your patch calls at the very start of the song, say in the first 1 bar or so, before any other song data starts. Then you can delete any patch calls from any individual loops you have, so the preset is never reset during the song. - This way the patch will retain any CC settings and tweaks that are made throughout the song, without reverting each time.
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