You can switch between any two materials without damaging the nozzle. If you mean flexible PLA, you will want to take it slow and make sure you know how to print with it as flex materials can be a challenge.
Did you open a support ticket regarding the previous change event so that you can learn what went wrong and how to prevent it in the future?
I personally find that when I change from one material to another, purging at the print temperature of the higher material works better than the average temperature that AutoMaker suggests. Even when going from PLA to ABS I will purge at 230 C so there is no problem getting the ABS melted and through the nozzle.
You will also want to make sure you purge every 10-20 hours with PLA and ABS to prevent material degradation.