Network Atlas stores all maps and other custom files (backgrounds, node images) in the Orion database in the table called MapStudioFiles. When the application starts, the files are synchronized with the content present in user's local folder in Documents And Settings (Application Data\SolarWinds\NetworkAtlas). If you delete the files from there, they will be downloaded from the database with the next start of the application.
It works the same way with the website, but the web server uses system Temp folder to store the files. This is usually C:\Windows\Temp, but it is based on your system's environment variables settings.
Please note that deleting the "temporary" files may hurt the application's or website's performance, especially the first start after the deletion. Also please note that any manual modifications to the tables may cause the application's malfunction.
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You explained that the files on the file system cannot be deleted, but it would have been nice if you also added instructions how to delete maps the proper way.
To delete maps:
Open Network Atlas, expand the Maps menu item in the left menu tree, right-click the map you want to delete and choose delete from the menu.
and how to import maps?
Can it be done by copying the exported maps (with the PowerShell script that was presented on TwackCamp2018) to the folder "user's local folder in Documents And Settings (Application Data\SolarWinds\NetworkAtlas)"?