Fixing Indices When Upgrading from 1.7 to 2.2

I am trying to upgrade from elasticsearch 1.7 to 2.2. However I am blocked from doing this by the incompatibility of some of my indices. I have used the Elasticsearch Migration Checker to look at and manage some of these, but others are closed, and I can't figure out how best to identify and correct all of these indices. I can't open all of them, as that would certainly crush the cluster, and I'm definitely not keen on deleting them.

Is there an optimal way to go through my indices and correct them to be compatible with elasticsearch 2.2??