Let me clear some things up.
1. The trademarks "Fatal Frame" and "Project Zero" are owned by TECMO KOEI GAMES CO., LTD.
2. Both Fatal Frame 4 and Project Zero 2: Wii Edition have joint copyright with TECMO KOEI GAMES and Nintendo.
3. All legacy IPs in the Fatal Frame franchise (Fatal Frame, Fatal Frame 2, etc.) are exclusively owned by TECMO KOEI GAMES CO., LTD.
4. There is absolutely no evidence, from Tecmo Koei financials, about the sale (or partial sale) of Fatal Frame assets.
5. There are, however, references to "joint Fatal Frame projects" that Tecmo Koei Games decided to do with Nintendo as the result of a co-development deal, including Fatal Frame 4, Spirit Camera, and Project Zero 2: Wii Edition.
Conclusion:
I have found nothing thus far to indicate that Nintendo co-owns any share of the Fatal Frame IP.
What Dantis believes is true---Nintendo only owns joint copyright with the projects they funded and collaborated with Tecmo Koei.