Glad you got it sorted! This doesn't seem to be too well documented...
Just for anyone else looking, it's the -s 0x08000000 that got you - since that overwrites the bootloader.
make clean && BOARD=PICO RELEASE=1 make flash
Calls st-flash not dfu-util for some reason, but it does choose the right base address so you can write directly without getting rid of the bootloader.
Or scripts/create_pico_image_1v3.sh will create the full binary (Espruino & Bootloader) which you can write to 0x08000000
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