After update to 10.1 most projects are gone

I just updated from FCP X to FCP 10.1
During the update it wanted to update all my projects and events to libraries. I did get a note about some missing files that may need to be relinked, but that's it.
However after the update, only one project made it to the Updated Projects folder. All the media (or events) are there, but the projects are not.
I didn't let the upgrade delete the old files, they are still there. Is there a way to redo the whole operation ?
How do I fix this ?

One of the drives is the Mac system disk. The other (archive) is a USB disk formatted as Mac OS expanded (translated from Finnish).
What is a root layer ?

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After update to 10.1 most projects are gone

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