tools and method to encrypt IP - VHDL RTL and IP-Netlist

This is probably quite a good place to start.

see the following solution and the links at the bottom

Altera do offer a DOS based encryption package for VHDL/Verilog which effectively creates a 'black box' design tied to a Quartus license. The software is called Ampcrypt and Amplic and you have to contact David Shih at Altera to obtain a copy.