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Yes, when HIDAPI is disabled, there is no popup and the gamepad does not work correctly. The same thing happens when connected via Bluetooth. 

Unfortunately, launching it first does not help, since the input from the gamepad after granting access is “fixed” in your app. For example, the same thing happens when a player requests exclusive access to DAC and the audio output is fixed to this player. 

Yes, "updated" /system/usr/keylayout/Vendor_057e_Product_2009.kl Unfortunately, this trick had no effect.

I'm not a developer, but I thought that maybe I could, for example, edit the Manifest in Citra emulator and compile the apk back. But if mapping database and other things are required, then it will be easier to just buy another gamepad. 

Thanks for the answer

The program works great, but in other testers and emulators the Pro Controller axes do not work correctly and some buttons are mixed up. Could you give me a hint on how to fix this Android problem? Your program requests access to the gamepad and thanks to this it works as it should, but other apps do not recognize the gamepad (access request popup). I replaced the keylayout file with an updated one, but it didn't change anything.