Hi Evertone,
I had recently updated my email id in Trailhead profile & dev org to match my Partner account with salesforce. But when i try to linked the new email id with the account, then it did not reflect all my badges. Also when i tried linking the old email id then the sync was successful with again less no.of badges. Seems the badges are tagged to the email ids. Some are with the old and some with the new. 
Also the salesforce partner community allows you to only add one salesforce trailhead account.

Thanks
Sumedh