Если elasticsearch установлен из deb-пакета на Ubuntu server, достаточно будет просто
$ sudo apt-get upgrade

или нужно следовать шагам из https://www.elastic.co/guide/en/elasticsearch/reference/curr..., а именно:
1. Disable shard allocation.

2. Stop non-essential indexing and perform a synced flush (Optional).

3. Stop and upgrade a single node.
To upgrade using a Debian or RPM package:
    -Use rpm or dpkg to install the new package. All files should be placed in their proper locations, and config files should not be overwritten.

4. Upgrade any plugins.

5. Start the upgraded node.

6. Reenable shard allocation.

7. Wait for the node to recover.

8. Repeat.
When the cluster is stable and the node has recovered, repeat the above steps for all remaining nodes.