Elasticsearch is never the primary for CommCare so unless you've also lost data in postgres / couch / riak it should be possible to rebuild everything. Your plan of blowing away all the indices and resyncing sounds right.
You can either run "./manage.py ptop_reindexer_v2 [datatype] --cleanup" for each affected index / datatype, or manually delete them in ES and then run "./manage.py ptop_preindex" to do it in bulk.