Yes.. you must be right. Maybe the best option for now is to keep this installation incident in mind, and if ever you find an error in your log.txt or encounter a sim crash somewhere in the world, try to identify the guilty corrupted files and delete them before running the installer again.
Or if ever you prefer to be sure your installation is clean, execute a sequence of installation, removal of regions little by little to reduce the risk of download failure.
One last thing, can you send your log.txt file (from the root of X-plane folder), so that we can check there is no unexpected error? This would confort the idea that the system files are clean.