In HA deployments Atlas instances load bootstrap types during initialization i.e. before leader election. When Atlas is brought up for the first time, this will initialize the store with the types defined in the model files.
Index setup kicks in when an instance is activated - GraphBackedSearchIndexer.initialize(); this looks for a specific property name ('__type') in graph management and upon finding it, Atlas skips rest of the initialization (creation of indexes like vertex_index, edge_index, fulltext_index). This results in subsequent queries to fail with error "vertex_index" not found.
The fix is to defer loading of bootstrap types to instance-activation.