Use Xilinx Vivado to create a new configuration for the programmable logic part of the Zynq7000 (PL) according to https://flink-project.ch/flink_vhdl#building. Result is a bit-file, e.g. flink2.bit.
Using Vivado, create a new Zynq7000 project following the instructions in 01_mzpz_zynq_intro_2016_4_01.pdf. Export hardware platform to SDK. We use this project solely for that SDK.