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I am uploading products via xls and this is working fine.I am uploading bundle/simple products

After that when all process complete. then I run bin/magento indexer:reindex by script for reindexing.

This deletes the bundle item data from mysql table catalog_product_index_price, and if I running bin/magento indexer:reindex using command prompt then this is working fine.

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My assumption here is that your script is not loading the correct area either cli or frontend and as such an event/plugin is not being loaded correctly.

What you could also consider is rather than calling the indexer via bin/magento you could inject the price indexer, something like Magento\Catalog\Model\Indexer\Product\Price into your code and call execute on that.

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