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ePWM Sync issue F28335

Hi, 

We are currently trying to control a dual active bridge and want to have Synchronized PWM's with the appropriate phase shift. ePWM3 should be in Synch with ePWM4 with 180 degrees of phase shift, ePWM5 should be in sync with ePWM6 180 degrees phase shift. ePWM1 and ePWM2 are used to drive an active front end and are in sync with each other.

Our problems occurs intermittently, when changing frequency of the Dual Active Bridge and doing a sync after each frequency change (Variable Frequency)...every so often the ePWM's go completely out of sync, it's random and we can't seem to figure it out. Has anyone had a similar problem? if so, is there a solution for it?