'System Software Missing' message at it's most benign and usual simply means that region 14 is either corrupt or empty. In such a state, there is no need to cure and remove files or reformat usually. Simply re-flashing original firmware is sufficient to restore fw_all.bin to rgn14 and allow the device to function normally. So try to flash ORIGINAL firmware but to do so you'll of course need to attain preboot mode. How are you trying to get into preboot? For zumo 660 you need to hold the lower (not the usual upper) left corner of the screen.
Note that if it's a problem with region 14 then the device usually defaults to preboot anyway. So the fact that you're unable to attain preboot might mean that it's a problem with the flash chip unfortunately.
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