How do I go about migrating an existing Solr instance (4.2.1) with several cores to SolrCloud (4.6.1)? Will I have to re-index the data?
If re-index is feasible - I would vote for it.
Unless you are specifically interested in DocValues, you don't have to upgrade the index format. See codec history here: https://lucene.apache.org/core/4_6_0/core/org/apache/lucene/codecs/lucene46/package-summary.html Make sure everything is backed up and indexes are in sync among replicas before trying.