Index replication and Load balancing

It seems that the best solution would be to index the documents on both servers into their own copy of the index.

If you are worried about the indexing succeeding on one server and failing on the other, then you'll need to keep track of the success/failure for each server so that you can re-try the failed documents once the problem is resolved. This tracking would be done outside of Lucene in whatever system you are using to present the documents to be indexed to Lucene. Depending on how critical the completeness of the index is to you, you may also have to remove the failed server from whatever load balancer you are using until the problem has been fixed and indexing has reprocessed any outstanding documents.

Basically you need two identical copies of the same Lucene index - one for each IIS server. I believe the simplest approach is to build an updated index on one machine, optimize it and then copy it to the other machine. On Linux I would use rsync, but I do not know the Windows equivalents. See Jeff Atwood's ideas for Windows rsync alternatives. Alternatively, you could issue the same index update commands to both Lucene indexes and verify they were processed properly. This is harder technically and only useful when you have more frequent updates. Please see Scaling Lucene and Solr for a broader discussion of distributed Lucene indexes.