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--flash_size 4MB-c1
for all 4MB board features
I tried
esptool.py --port COM4 --baud 460800 write_flash --flash_freq 80m --flash_mode qio --flash_size 4MB-c1 0x0000 "boot_v1.6.bin" 0x1000 espruino_esp8266_user1.bin 0x3FC000 esp_init_data_default.bin 0x3FE000 blank.bin
so
esptool.py --port COM4 --baud 460800 write_flash --flash_size 4MB-c1 --flash_mode dio 0 .\espruino_1v99_esp8266_4mb_combined_4096.bin
Please check post #10 and add this option to the flash command.