Hi Jeff,
Turns out I'm also trying to get a USB CDC host running on OTG2 on an RT1052, though I'm not looking to switch back and forth. So far, I'm not having success... the USB ISR never fires. I'm not convinced that the MCUX configurator is creating the correct settings for which EHCI controller is associated with OTG2, I'm still debugging and will probably create my own post. I'll update here if/when I do.
Frankly, I'm not impressed with the CDC host middleware that's provided; it's badly cobbled together from the USB CDC bare-metal SDK example, and doesn't do anything useful as provided. It should provide a clean API for applications to get USB in data and send USB out data, but instead you have to hack apart the CIC functions they give you. There shouldn't be any reference to a "UART" in the CIC code, but there's dozens still there because they just ported the SDK example and left all the confusing variable names in place.
To your original question... I don't think it should be that big a deal to switch back and forth. There are USB_HostInit() and USB_HostDeinit() calls in the API, so I would think you should be able to simply shut down the one interface and then start the other. You would just need to make sure you're passing the correct instances to your event handlers and ISR.
David R.