Restore from iCloud duplicated file structure

We replaced a MacBook Pro that was working with Box in Finder and Syncing fine. We backed up the old MacBook Pro to iCloud and then restored onto the new MacBook Pro. There is only two of us that share files but what became obvious was that we couldn't see each others files. On the restore Box has downloaded or synced the whole previous folder structure but has duplicated the folders. What happens now is that I am uploading files to the folder that my partner cannot see and vice versa.

In Finder she can only see the new but named the same yellow folders which she is updating to but cannot see the shared folders that we used to use.

She is still visible as Editor on all the 'blue' folders you see when you access Box through Safari

Any clues on how we sync the duplications and subsequently delete the duplicated folder structure?

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