When using Block Level Incremental Synthesis (BLIS) flow with FPGA Express, design constraints which would normally be written to a .NCF file are instead written to a .SCF file. The .SCF file is not automatically read by the Xilinx implementation tools, therefore the user must copy the contents of the .SCF file into a .UCF file in order for the constraints to be passed forward.
Solution
Cut and paste the contents of the .SCF file into the project's .UCF file, or rename the .SCF file to a .UCF file.
Do not simply rename the .SCF file to .NCF, as the file is not a legal NCF file and will create errors in NGDBUILD.