Ok, it's hard to explain a step by step repro path... I'll try to make a video or finally report detailed instructions.
I've noticed this once I tried to add as 2nd remap list for port2=Joystick (attached my Hori Fighting Stick Mini) some buttons to P, Space, Return for some games... Once I returned in game they didn't work, or WinUAE forgot some others secondary remapped assigned keys I had previously set etc. then I noticed those apparently disappeared remaps did show up again in the GUI after I scrolled up/dow etc. a mess to explain
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