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The flash module appears to work, so I doubt anything is wrong with SPI interface.
The code above that worked is writing internal nrf52 flash, not SPI flash. Something was probably wrong with SPI flash at that time - you got the " InternalError: Timeout on jshFlashWrite at line 1 col 44" which looks like bad communication over SPI. Anyway, looks like it is working now.
fanoush
@Mark_wllms
Thanks @fanoush. The flash module appears to work, so I doubt anything is wrong with SPI interface. I know storage module does wear levelling, so I assume it caches its state somewhere, and maybe that has become corrupted. Is there a way to wipe the storage entirely and start again? I tried, but managed to wipe the bootloader instead!