I have 5 different apps with different index on each apps and with same sourcetypes every apps. I have different calculated fields every apps that has only "per app" permission and my 6th app will be my main app that will search all my index. How will I apply my calculated fields on my 6th app when i make a query of different index. To explain more further, i will have this example...
you could try to create a calculated field for each app from the original field with a different name (e.g. myfieldapp1) with global access properties.
Then you could use, in the sixth app, the new calculated fields, eventually renaming them, in your searches.