Elasticsearch ignores old data after upgrade from 1.7.3 to 2.3.0

First, I've tried this on local machine.

  1. Installed ES 1.7.3
  2. Populated it with some production data
  3. Installed ES migration plugin
  4. Reindexed data and deleted old indices, so migration plugin showed that everything is ok
  5. Upgraded ES to 2.3.0
  6. Restarted ES

Everything worked and I was able to query all indices.

I used the exact same procedure to upgrade ES in production. Unfortunately, there are issues.

Elasticsearch 2.3.0 is green and running, but it ignores indices. Currently it shows only 3 indices - 2 for marvel and 1 for kibana. I'm sure that data dir is correct - these indices stored in the same place as old ones.

Logs show "dangling index directory detected, but no state found" for each old index.

What should I do?