I booked my trip directly through the WDW UK site a little over 500 days in advance. I was given a reservation number, but was unable to link it immediately to my MDE account. So, I contacted the Disney people who said something along the lines of that bookings made in the UK need time to reach the US systems or something and since I was booking far in advance, mine wasn't being prioritised. However, they told me that if I couldn't link my booking by the 200 days to go point, I should get in contact with them. As it happened, I was able to link my booking a few months later.
So, to cut a long story short, if you have not been able to link your booking immediately, do not fear; the reservation is still present. If you haven't been able to link it by the 200 days to go point, then get in contact.
Hope that helps!