I don't think any data protection rule (I don't even know which one you're talking about) would take out certain peering between europe and asia - and happen completely unnoticed at the same time.

Just as few examples:
If I trace to yahoo.co.jp, which is also located in Tokyo, Vodafone's peering partner Cable & Wireless forwards it to IIJ (Internet Initiative Japan) and the connection is fine.
Tracing to Livedoor.com, also Tokyo, Cable & Wireless forwards to NTT, and its also fine.

Fortunately, after some search, I found another endpoint (www.nli-research.co.jp) that uses a Cogent path from europe - and that site is also "almost" unreachable. So I'm pretty sure the issue is at Cogent and nowhere else.