Going to the nether and coming through the portal could delete the player's Overworld data.

What's the player's overworld data ?

making my head hurt

I'm guessing, which is a wild guess since there is no actual post, the this person is on SMP and wen't to the Nether and came out through a synced portal and thinks his stuff is gone. That would be intended behaviour afaik.

Ticket resolved as incomplete, because no answer in a reasonable amount of time (1+ year), if it still happens, please update the ticket.