You can stop DMA safely using
CyU3PDmaChannelReset() and CyU3PDmaChannelDestroy().
Also if you want to flush the EP then you need to use CyU3PUsbFlushEp.
This is what we have used so far and it is working fine for us.
If it is not working still then please create a Technical support case by attaching your project code.
Our guys will look into it.