That sounds very much like failure of the flash memory.
https://www.mobileread.com/forums/sho...49&postcount=3
The changes seen in what is stored (or not stored) are the result of the system caching disk operations.
Anything which clears the cache (such as restarting) shows the (un-changed) content of the flash.
One thing worth doing, check the serial number of your device (if the kindle isn't working, you can find it on your Amazon account page) against this table:
https://wiki.mobileread.com/wiki/Kindle_Serial_Numbers
Just on the chance that your device isn't a PW-2 (which would explain only why the 5.6.5 update disappears, not the rest).