Looks like you're using the query within stored procedure which migh span across multiple pages, you need to use the continuation token in that case. You can look at this example below,
function tryQueryAndDelete(continuation) { var requestOptions = { continuation: continuation }; var isAccepted = container.queryDocuments( containerLink, query, requestOptions, function(err, retrievedDocs, responseOptions) { if (err) throw err; if (retrievedDocs.length > 0) { tryDelete(retrievedDocs); } else if (responseOptions.continuation) { tryQueryAndDelete(responseOptions.continuation); } else { responseBody.continuation = false; response.setBody(responseBody); } } ); if (!isAccepted) { response.setBody(responseBody); } }