Flashing with QMK Toolbox stopped making changes to keyboard layout

I made a new layout (see here: my qmk_firmware fork) for my Iris, compiled it in WSL and flashed with QMK Toolbox several times, for several iterations of the layout.

At some point, flashing stopped making any difference. I see the regular success logs in the Toolbox (see below), but the previously flashed layout remains operative.

I also tried flashing the default 'via' Iris layout for comparison, but I'm still stuck with an older iteration of my custom layout.

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Toolbox logs:

*** Atmel DFU device connected (libusb0): Atmel Corp. ATmega32U4 (03EB:2FF4:0000)
*** Attempting to flash, please don't remove device
>>> dfu-programmer.exe atmega32u4 erase --force
    Erasing flash...  Success
>>> dfu-programmer.exe atmega32u4 flash --force "Z:\home\niv\dev\qmk_firmware\keebio_iris_rev4_gelbermann-colemak.hex"
    Checking memory from 0x0 to 0x6FFF...  Empty.
    0%                            100%  Programming 0x5200 bytes...
>>> dfu-programmer.exe atmega32u4 reset
    [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>]  Success
    0%                            100%  Reading 0x7000 bytes...
    [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>]  Success
    Validating...  Success
    0x5200 bytes written into 0x7000 bytes memory (73.21%).
*** Atmel DFU device disconnected (libusb0): Atmel Corp. ATmega32U4 (03EB:2FF4:0000)

Compilation logs:

Ψ Compiling keymap with make --jobs=1 keebio/iris/rev4:gelbermann-colemak


QMK Firmware 0.14.9
Making keebio/iris/rev4 with keymap gelbermann-colemak

avr-gcc (GCC) 5.4.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Size before:
   text    data     bss     dec     hex filename
      0   20994       0   20994    5202 .build/keebio_iris_rev4_gelbermann-colemak.hex

Compiling: keyboards/keebio/iris/keymaps/gelbermann-colemak/keymap.c                                [OK]
Compiling: quantum/via.c                                                                            [OK]
Linking: .build/keebio_iris_rev4_gelbermann-colemak.elf                                             [OK]
Creating load file for flashing: .build/keebio_iris_rev4_gelbermann-colemak.hex                     [OK]
Copying keebio_iris_rev4_gelbermann-colemak.hex to qmk_firmware folder                              [OK]
Checking file size of keebio_iris_rev4_gelbermann-colemak.hex                                       [OK]
 * The firmware size is fine - 20896/28672 (72%, 7776 bytes free)

I'm fairly new to using QMK directly, mostly used Via until now, so the layout code definitely has issues, but I've had several iterations working OK so far, so I don't think the issue is in my code.

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I'd appreciate any assistance!