Timers, PWM pins and digital outputs on Arduino Mega
You can use them for any purpose other than PWM.  You can even use them for PWM as long as the settings for the timer allow you to produce the waveform you want.
The reason PWM broke was that you had changed the settings for the timer.  The timer is what controls the PWM.  When you changed those settings you either turned the PWM function off or set some setting where it wouldn't work.  Then the pins associated with that timer didn't get PWM anymore.  You can do anything else you want that doesn't involve the timer including use the pin for input or output or any other special function it has not related to the timer.
If you change the timer interrupt to TIMER0, then you run the risk of delay, millis, and micros stop working right.  They depend on the TIMER0 overflow interrupt running at a set interval to count time.  It depends on how you set the timer up.
I would suggest you do some reading on how these timers work.  The Datasheet for the ATMega328P chip is a great place to start.