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I've just started #361 which hopefully addresses your previous issues. As for this, I copied this workspace to my local DB this morning and I saw a few duplicates (not as many as you have, though), however those duplicates actually exist and the quickest remedy on build #361 was to delete them and they haven't appeared again. When #361 is merged and published I will notify you.
Edit: I've just downloaded it again and I see this on my local build, so I hope that that will fix it:
Yes, I can also see in the workspace that there are several duplicities (e.g. in "má vztažený prvek 1/2"). Even if I remove them, they appear again after reloading the workspace.
In "OFN Časové okamžiky a intervaly" (https://slovník.gov.cz/datový/pracovní-prostor/pojem/metadatový-kontext/instance-1764959588), tab "Časový interval". When I choose "Časový okamžik" and then "Vazby", I can see a given relationship type shown several times:
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