Hi Mathew,
I migrated IndexServer from 5.3 to 6.5 on Windows Platform.
While migrating IS .I configured IndexAgents in migration mode for indexing old doc's and deleted those migration IndexAgents ,
configured in Normal mode for current version(6.5).
After deleting the IA in migration mode ,where the Indexes will going to Stored.
They will be stored in docbase (or) Index Server or any other location.
Thanks in Advance
laxmi