Well, yes, an electronics chip of any kind can incur permanent damage due to overheating.
But on page 17 of the manual
it says the chip self-protects against overheating by shutting down until the die temperature has dropped enough to operate safely again.
And almost invariably the damage from overheating (if it really happens) destroys the normal functioning of the device permanently. That is, it completely stops working. So if your motors all move back and forth and sound normal while doing so, then it's almost certain that the chips were not damaged.
Have you checked all the chips for heat? Maybe only one is overheating.
Maybe when you messed around with accel values you ended up asking the chips to perform in a way that was impossible for them. There are timing requirements on page 7 of the manual, including a maximum step frequency of 250kHz. If you're pushing the chips near the limit of the step frequency, then they'll end up burning a lot of heat internally just trying to keep up. Do you know how many microsteps you are using? What's the voltage rating of your motors? If it's too high, then the chips never get really good control of the motor current during moves; I recommend motors with a voltage rating of 2.8 volts. The chips control motor current, not voltage, and a motor with a lower voltage rating gives the chips more "headroom" to play with when changing the current (motors are inductive loads, and the nature of an inductor is to resist changes in current by exerting a counteracting "reactive" voltage).