It looks like fears of a violent clash have been averted for the moment, with the spotlight on Hunt Oil's operations, the oil company and Peruvian government have agreed to talk with the local indigenous communities rather than pretend they just did not exist. Some good resources below, Terry Wade's Reuters piece explains the competing claims of the different parties better than anyone.
RPT-Peru tribes pressure Hunt Oil to leave Amazon, Reuters Terry Wade
Amarakaeri natives begin a massive sit-down demanding Hunt Oil Co. to leave their territory, Living in Peru
Crisis averted for now, Peruvian natives will meet with Hunt Oil, mongabay.com
The Harakmbut: Defending The Amarakaeri Reserve, Amazon Watch
Indigenous Peoples Of Amarakaeri Communal Reserve And Hunt Oil Company: Background Information, Indigenous Peoples