slighty wrong
As already explained in the wiki, any restore package or root package is applied as follows:
1.) Fully charge reader
2.) unzip the package on pc
3.) connect reader to pc and select data transfer
4.) run the flash bat
on PC. the flash bat will copy necessary files to the reader
5.) type y+enter
But if you applied sony update you definitely don't have your reader rooted anymore.
I suspect that it is the data partition that causes trouble for you, there may be some apps left on it.
Again, I advise you to make a factory reset and see if it helps:
https://wiki.mobileread.com/wiki/PRST...#Factory_Reset