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Hi there, please find the answers inline
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Yes it is a resource intensive operation and it is recommended to trigger it off business hours or low traffic times. It triggers an asynchronous task that will run in the background until the job is done. You might still be able to perform queries on your cluster while force merge is running if resources are available. But most often all requests are blocked during that time.
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As of now there is no work around to eliminate the deleted documents. Segment merges remove this deleted documents automatically when it runs. But to avoid cluster running segment merges when indexes are receiving writes, you should execute force merges periodically when indexes don't receive any write.
Hope this helps!