a. When you create different DMA channels, are the separate DMA channels interconnected? In other words, can one DMA channel cause another DMA channel to hang?
No, the DMA channels are not interconnected. Please check if there are any blocking calls in any of the DMA callback handlers. Ensure there are no uart debug print APIs called.
After calling CyU3PMipicsiWakeup(), if timer is triggered, then you will have to check why there is no data coming from GPIF for 200ms (which is the time out period of the timer). As part of RESET_EVENT handler, please check if you are also resetting channel corresponding to EP1 - and check if any of the code in here is related to EP1 communication.
b. Is there a proper way to create a second DMA channel with the CX3? We have created multiple DMA channels with the FX3 with no issues.
There should be no difference in DMA channel creation between FX3 and CX3.