One of the other options you have is indexdefrag. A reindex will rebuild the entire index in a single transaction that locks the table and only commits once it is done. If you are rebuilding the clustered index, all non-clustered indexes will rebuild since they point at the clustered index. There isn't anyway around it using a reindex since log shipping can only apply committed transactions and a tran log backup will only take up to the oldest open transaction. An indexdefrag rebuilds the indexes as well using a series of "micro-transactions" which allow for the terminate of the indexdefrag without losing any work performed and it also will move the data to your secondary much more quickly, thereby reducing the latency.
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