In my project, I still use a Cyclone IV FPGA and a MSC4 config memory.
There is a way for programming the FPGA with a new version of configuration program, distributing the new release to final customer whitout that the user can see the program code (written in VHDL)?
Can you provide the exact memory part number? Which device are you using ? EPCS/EPCQ?
Do you want to configure the FPGA / config memory without exposing the underlying VHDL/Verilog source code at the end-user side? If this is the case, then all you need to provide to the end-user is the compiled SOF/POF files and have the end customer download only the Quartus Programmer standalone version and get the USB Blaster/Blaster II cable. With this setup, all you need send the customer is the compiled output POF/SOF files and show the customer how to program/configure the device. You will not need to send / expose the source code in this case.