UE4.1 VS deletes Android dlls as junk, no Linux package option

First, I would suggest getting the latest cross-compiler from the official release, as it may have been updated since the preview build.

Second, the GitHub source is not intended to be extracted into the Launcher version, and doing so will lead to bad times (as you discovered). Instead, extract the GitHub version to it’s own location and follow the instructions in the readme on getting started.