Instead of preventing flash erase you may include bootloader image in your project output files (S records files and *.abs ELF file). To do so you need to
1) copy bootloader S-records into project \bin folder. I guess any folder from project access path will work.
2) add line to prm file
HEXFILE bootloader_S19_file_name.s19
Multilink/Cyclone connection has AEFSKIPERASING command, which can be added into one of *.cmd files. This commadn allows to skip erase of whole flash blocks or EEPROM blocks. This is not what you want. I guess flash loader uses mass erase command instead of erase sector by sector. Mass erase is faster. If that's the case, then flash protection won't help here, because mass erase doesn't work if any portion of flash array is write protected.