Documents version getting set to -1

We are migrating ES from 2.4 to 5.6. Before migrating we copy all the documents from Index A to Index B. After migrating to 5.6 we are seeing many of the documents version on Index B is getting set to -1, hence the delete by query fails to delete these documents. Also the GET api returns found as false on ES 5.6 although we can see the document on the index. While copying the data from Index A to Index B we are using the default internal versioning. Request any inputs on this.

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