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I've made a small tool to fix maps once you've move your hexagons to a subfolder.
It will look for the new hexagons folders, and update the map accordingly.
It will only find the hexagons if they stay in the same collection.
It works on Linux for my maps. I haven't done any test on Windows or MacOS.
It is an early version. So be careful.
Dot not erase your original maps.
Hope that helps.