Mapping conflict resolution

I am planning to upgrade my ES cluster from 1.x to 2.x
Earlier, I had 2 types in a single index which had the mapping conflict.
So, I planned to break the two indices into separate indices, which resolved the mapping conflict issue.

And, then I had setup an alias which points to both the indices.
Now, the problem is aliases allow only _search APIs. So, I am kind of stuck right now.
If I can not use the alias name, then that would mean lot of changes in app code.

Thankfully, I have done all this on y staging cluster and not production.
What is the best way to go around?

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