I realised that when moving documents between databases they only keep the directly set tags. Tag hierarchy is not preserved. I understand this behaviour. However there are cases when I need to
replicate the complete hierarchical structure of my tag system between databases. Or more precisely: to sync all tags including hierarchy. Is there any sane simple way to do so?
You could duplicate the hierarchy but replicating isn’t possible (just like Unix hard links are limited to one volume).
Having just been bitten* by this. The behavior as-is seems to violate the most fundamental covenant between developer and user: don’t destroy information without the user’s express knowledge and permission. With that in mind, I have a question and a suggestion.
The question: Why aren’t tag hierarchies preserved across databases? Corollary: why bother nesting tags if the feature isn’t important enough to preserve across databases?
The suggestion: Please give us a heads-up when metadata will predictably be lost as a side effect of a seemingly unrelated operation. I understand there may be something in the docs that explains this behavior, but it’s unrealistic to expect new users to digest the entire User Manual prior to making use of the application…let alone to remember everything encountered therein. 
*My use case is idiosyncratic, so I won’t go into detail except to say that I’d just meticulously tagged hundreds of files with a tag hierarchy in the global Inbox, and was shocked to see that hierarchy squashed flat upon moving a subset of those files into a new database. It’s not a complete waste as I’ll be able to recreate the hierarchy by dragging tags onto each other, but it’s not the most productive use of my time. ¯\_(ツ)_/¯
It’s a known shortcoming as the existing tags of the target databases are reused first. But the tags in this database might be organized completely different, even the settings (see File > Database Properties…) could be different and can have a huge impact. But it’s planned to improve this in upcoming releases.
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Good to know. Thanks!