I am using pk2cmd command line tool for pickit2, which has options to
program only code space or eeprom, but it fails verification always if
option other than "delete/program all" is selected, it complains about
some particular address when data is not as expected. I tried with
different chips with the same result.
The very least thing I was hoping to achieve was that eeprom would not
be erased at every code change.

>
> I don't know if it's the same with Linux, but on Windows using the
> PicKit2 software you can program the EEPROM directly (on it's own if you
> want) by just typing the values required into the EEPROM data window,
> then hitting write (untick the "enabled" box next to the program memory
> window if you don't want to program that too)
>


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