All the Prepar3D versions of Draken are installed in separate folders within the main Bookmark Simulations add-ons folder and will not affect each other. Patches/hotfixes that are issued between the release versions will normally overwrite files in the current installation.
Draken 4.1 for FSX is installed in its own aircraft folder and in sub-folders within the main FSX gauges and sounds folders. The effects files are specific to each version and will not conflict with previous versions. The included scenery files will be updated from earlier installations and are fully backward compatible.