Using Add Alias_Alias and Alias Folder.vi in a loop with many aliases in the same path will result in a sysdef with just the last alias in the folder. This is because the Add Folder subvi is set to "Overwrite" by default.
Compound Issue:
When set to "Not Overwrite" the underlying VI returns an error that the Node already exists. This basically means you cannot add multiple leaves under the tree.
Recommend
Update the case where "Overwrite" is false to handle changing a given node. Although this might have to be made specific to Folders since updating an Alias as a leaf would be an entirely new set of functions, unless that "just works" we can test that.