Carlos -
We've have the same issue with KDS that Josh reported, and we have tried using the "Flash from file" option but it has the same problem. We're using KDS1.1.1 and we use a P&B USB Multilink.
How did you set up your configuration in order to get this to work for you?
Here's what the tail part of our Console looks like when doing the "Flash from file:" (I have trimmed some of the blank lines) and you can see it still does a mass erase.
CMD>PM
Programming.
Processing Object File Data ...
Programmed.
CMD>VC
Verifying object file CRC-16 to device ranges ...
block 00000000-000001DF ...
Ok.
block 00000400-0003957B ...
Ok.
Checksum Verification Successful. (Cumulative CRC-16=$7A8F)
CMD>RE
Initializing.
Device is Secure.
Device is secured. Erasing ...
Target has been RESET and is active.
Disconnected from "127.0.0.1" via 127.0.0.1
Terminating Gracefully...
Target Disconnected.