While it's true the code configurator includes pre-built modules into the code, it does it at source code level so it is still easy to edit it before compiling. It is a utility to speed up the programming process, not to make it more secure.
If you have doubt about the software engineer's motives but you are not confident to check it yourself, get an independent third party to check it over. I will say this though: if the product doesn't have a real-time clock in it or some other method of checking operational time, it's far more likely the failures are due to EEPROM endurance or an electrical problem. A time bomb in software isn't unheard of but unless this contractor is about to go off the radar, they should still be liable for the consequences of their errors and misdeeds.
Do you know what actually stops the product working properly, for example, does replacing the PIC cure the problem every time and what happens if you compare a new and used device, there would have to be a difference in memory contents.
Brian.