I'm designing a a BLDC controller and came to think about fail safe in case the controller crashes/freezes.
Current plan is to use one timer/pwm to charge parallel capacitors with bleed resistors and a nand gate to control the ir2104 enable input.
My specific question is: Is it possible that a timer keeps running if the MCU freezes/crashes/hangs for any other reason than code getting stuck on loop?
If failure of your motor control could cause harm or death to humans or animals, I would recommend you investigate products that were designed for safety critical systems.
Otherwise, I would recommend you build your motor control and power hardware in a way that the system is save no matter what the state of the control pins are (input, output, tri-state).
Regarding your question, yes, a PWM peripheral will create a PWM signal even if the software does not write to it anymore. The most likely case is a constant duty cycle. You could imagine a system where the duty cycle is updated inside an interrupt service routine and therefore the pattern could be different.
As jremington recommended the use of a watchdog can help if properly implemented.