Is there any way to merge data collected using 2 different Tracking IDs of Google Analytics?
Using the Google Analytics API you can extract the data you wish from both properties into your own system. Say a database I recommend adding the property id to the tables storing the data so that you will be able to differentiate between the data.
There is nothing out of the box that will do this for you with the exception of big Query. Users with a Google analytics 360 account can extract there data to big query. However I have not tried this I am not sure even that will allow you to analyze data over multiple views.