SPIFlashWrite is called when WiFi config is changed. If you are joining the same network, you don't need to call WiFi.begin, SDK will join the last network without writing anything to flash.
Flash is also written when using SPIFFS, EEPROM, and doing OTA.
By the way, this is related to #836. As a summary, PWM needs the following things fixed:
move timer handler and PWM routines into RAM (need to free up some RAM to do that, possibly by removing espconn from liblwip.a, or moving some strings into flash)
use NMI instead of regular interrupt
refactor existing critical sections in PWM routines
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