Swapped Backspace and Space and on function layer too, but function modification does not stick

I swapped the Backspace and the Space keys using the Ardunio IDE. I also want to swap the Enter and delete key so that the delete key is on the right also just like the backspace.

I set a custom layout PRIMARY_KEYMAP_CUSTOM) like so which works.

  (___,          Key_1, Key_2, Key_3, Key_4, Key_5, Key_LEDEffectNext,
   Key_Backtick, Key_Q, Key_W, Key_E, Key_R, Key_T, Key_Tab,
   Key_PageUp,   Key_A, Key_S, Key_D, Key_F, Key_G,
   Key_PageDown, Key_Z, Key_X, Key_C, Key_V, Key_B, Key_Escape,
   Key_LeftControl, Key_Spacebar, Key_LeftGui, Key_LeftShift,

M(MACRO_ANY),  Key_6, Key_7, Key_8,     Key_9,         Key_0,         
Key_Enter,     Key_Y, Key_U, Key_I,     Key_O,         Key_P,         Key_Equals,
              Key_H, Key_J, Key_K,     Key_L,         Key_Semicolon, Key_Quote,
Key_RightAlt,  Key_N, Key_M, Key_Comma, Key_Period,    Key_Slash,     
Key_RightShift, Key_LeftAlt, Key_Backspace, Key_RightControl,

Then I also wanted to do the swap on the function layer by doing the following:

  (___,      Key_F1,           Key_F2,      Key_F3,     Key_F4,        Key_F5,           
   Key_Tab,  ___,              Key_mouseUp, ___,        Key_mouseBtnR, 
  Key_mouseWarpEnd, Key_mouseWarpNE,
   Key_Home, Key_mouseL,       Key_mouseDn, Key_mouseR, Key_mouseBtnL, 
    Key_End,  Key_PrintScreen,  Key_Insert,  ___,        Key_mouseBtnM, 
 Key_mouseWarpSW,  Key_mouseWarpSE,
   ___, Key_Enter, ___, ___,

   Consumer_ScanPreviousTrack, Key_F6,                 Key_F7,                   Key_F8,                   Key_F9,          Key_F10,          Key_F11,
   Consumer_PlaySlashPause,    Consumer_ScanNextTrack, Key_LeftCurlyBracket,     Key_RightCurlyBracket,    Key_LeftBracket, Key_RightBracket, Key_F12,
                               Key_LeftArrow,          Key_DownArrow,            Key_UpArrow,              Key_RightArrow,  ___,              ___,
   Key_PcApplication,          Consumer_Mute,          Consumer_VolumeDecrement, Consumer_VolumeIncrement, ___,             Key_Backslash,    Key_Pipe,
   ___, ___, Key_Delete, ___,

However after doing the following change, the keys on the functon lay are still in the original position aka not reversed, after flashing the firmware successfully multiple times.

Am I editing the wrong layer? I also made some Lighting modifications to limit the choices, should not effect FUNCTION layer, but maybe I messed up something. please see attached ino file. Also Firmwarre version 1.96

Model01-FirmwareCustom2.ino (21.5 KB)

As an update, I managed to swap the Function layer keys with Chrysalis. However if I try to flash the default firmware from Arduino, everything reverts except for both the swapped keys on primary layout and on the function layer too. Not sure why this swap is defying logic by the Arduino firmware flash.