STM32 Programming

Hi all.
I have a STM32f100C6T6B micro-controller fitted to cable operated length sensor.
To replace this chip can i simply use the ST Link Utility to download the files from the old controller remove and replace and upload on to a new one.
I ask this having already tried and does not seem to be the case. The output from the sensor should read 0.5V fully retracted to 3.3V fully extended. The sensor would not output anymore that 0.5V before the replacement. But now will not read any voltage after replacement. Am confident that no damage has occurred to any circuitry while replacing. The inputs to the controller are present, giving the same readings as before.

Many thanks