Unique ID counter

[ScaleRobotics]

If they are all to carry the same firmware, you can have Microchip program them for you, for a fee. They can program a unique serial number using their Serialized Quick-Turn Programming (SQTP) . But, it might be cheaper to buy a MeLabs programmer

[pedja089]

If you are good in windows programing, try to create VBS, or some .exe, that will change that values in hex file, and send it to programmer, using command line option to start programmer.
It should be easy job...
Something like this vbs

Dim i as integer
strbuff as string
For i = 0 to 65535
Open SorceHexPath For Input As #1
    Input #1, strbuff
Close #1

'Find & Change eeprom value

Open EditedHexPath For Input As #1
    print #1,strbuff
Close #1
Shell programerpath -pPIC etc....
Next i