You could write a Cordova wrapper for your native code, if they access native APIs.
If I understand your question, though, the answer is that you can not route some views to Ionic and some views to native. Cordova is a WebView itself, and trying to mix the webview layer with your custom native layer views would be quite difficult to implement with so many moving parts.
My recommendation is to convert it all to Ionic, because it is more maintainable and easier to update.