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3) I open the FPGA project of the Second Application and replace the EPCS bootloader in SOPC builder and build again.
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Each time you regenerate your SOPC builder system it will overwrite the hex file with the default boot loader. After each time you regenerate the SOPC builder system you need to copy your compiled boot loader hex file over the default one before compiling the Quartus project.
If you are just trying to replace the boot loader, you can avoid a complete Quartus recompile by just copying your boot loader hex over the old one then do a "Update Memory Initialization File" followed by "Start Assembler".
Honored Contributor
