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My customers are using software that rely on folder structure in data folder. A lot of them are empty, and being populated with data at some stage. When restoring, only folders that are not empty are there and software refuse to work.
Also i can see potential problems in the future with backup/restore as i am expecting to restore data to exactly same condition as time of backup - that includes any empty folders (names might be an importand data), hidden/system files etc..