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Please see the official X‑Plane Support page for help.
The missing scenery alert should tell you exactly what tile you are missing. Can you confirm it is actually missing from your global scenery folders?
Please run the installer again and make sure the area you're missing is still selected. Progress through the download (if applicable) and then check your X-Plane global scenery folder to see if the file has been replaced. The installer is supposed to realize it's missing and replace it.
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