The use of "chips" programmed with internal software (also called firmware) is wide spread these days.
Security fuses inside these microcontrollers dictate wether a third party can read the "firmware" with a programming tool.
Or not...and that is a very attractive way for a company to control the market.....
Microcontrollers and their embedded firmware are normally very reliable (lightning strikes excluded)
In my experience most failures on a PCB have to do with the periferals that connect the microcontroller to the outside world: drivers, control lines, protection devices and power supplies.
One can often roughly tell what the function of a "chip" is just by looking at its number, then download its datasheet on the internet and measure if it works correctly.
Avaiable for help, I hope this information is usefull in some way.