The FSDT Live Update DOES NOT touch any of the files related to the scenery library and it won't change any of the files in the sim. It will ONLY update whatever FSDT files you already have installed so, I don't see how it's possible that running or not the Live Update would make any difference to your ability to edit the scenery library.
This, assuming your report that "just" using the Live Update will cause this. However, your reference to "manually add all the FSDT sceneries" seems you really meant something different, as if you manually added the sceneries using the old method, which adds the sceneries to the scenery.cfg rather then using the add-on.xml method so, rather than Live Update, maybe you meant the new installers which use the new method.
However, be careful with "manually adding" because, the installer obviously add the areas already correctly so, if you added them to the scenery.cfg too, you might introduce a conflict this way.