After a Teamviewer session with albix, we think to have found the cause of this problem:
There was no issues with the updater and no problem with the scenery, which worked fine alone.
It was a conflict with another scenery. We haven't found exactly which one but, the problem is, many 3rd party sceneries are using a file named modelLib.BGL, with an override in their own package folder for the Scenery\Global\Scenery folder.
We tested this not to be a problem with some other sceneries installed that have the same file, so we assumed it's not a problem. But apparently is, if too many add-on use this name.
We fixed it by renaming our file to FSDT_KORD_modelLib.BGL, running the FSDT Live Update will fix the filename for everybody.