Hi,
The problem with Unity 2017 is that it's a new iteration and it come with few issues unfortunatly, one of which seems to be that that some assets don't get imported properly, yet flagged as such and so Unity just thinks it's fine, yet you would really need to run the api updater, the only solution is what you did, just keep shaking Unity until all files are properly imported.
I always recommend that on sensitive projects that major versions are always left for toying around, I would wait for 2017.2 or even 2017.3 really, and meanwhile simply make copies of your project and see how it behaves with the latest version of Unity and move your way up like that.
Bye,
Jean