DesignPackage.Install method is clearing up the entries from the composed looks list on the root site

We are trying to upload and activate a custom site template to the solution gallery of a site collection. When we use the DesignPackage.Install method, it is activating the solution on the site collection, but it is emptying the entries on the composed look from the root site.

Is it a known issue? Do we have any other way of automating this step?

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Vijayaragavan, MCTS