It's not possible the unencrypted version .BGL downloaded by the FSDT Installer could cause any problems to the simulator, because it's installed in the %APPDATA%\Virtuali\GSX folder, so it's something that only GSX will see or use
The simulator itself won't ever use anything that is not located in the Official/Community folders, either directly or by using Symbolic Links, but surely we don't link the %APPDATA%\Virtuali\GSX folder so, unless you created that link yourself, you can be sure the simulator won't see that file so, if the sim crashed, it couldn't possibly be caused by the unencrypted version .BGL downloaded by the FSDT installer.
It MIGHT be possible the crash might have been caused by the scenery downloaded from the Marketplace: it already happened once ( with the Swiss Mesh ), that we sent a perfectly fine unencrypted file to Microsoft, which for some reason became corrupted when user downloaded it from the Marketplace, as if a problem happened during the encryption, which is a process completely outside our control.
If we'll get other similar reports, we might investigate this further and report it to Microsoft. Just to be confirm: are you using a PC or an Xbox ?