I don't think you can do anything in Geany itself.

I don't know how this re-mapping works but I would expect it just sends different key codes to applications so I would expect this to be transparent to applications. Geany is a GTK application so maybe one thing to try is to look for GTK problems of this kind.

Also, in GTK it is possible to remap keys using GTK key themes so you could play with those too (you just have to check if Geany was compiled as a GTK2 or GTK3 application and look for the right documentation for your GTK version).

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