Due to a problem in the Quartus® II software versions 10.0 and 10.0 SP1 for Linux, a Hexadecimal (Intel-Format) File (.hex) may appear as read-only even though the owner has write permission for the file. This may prevent you from saving any changes to the file to the same file, or even from saving to another .hex file, or as a Memory Initialization File (.mif).
To work around this problem, ensure that the .hex file has write permission for all users before opening the file in the Quartus II software.
This problem is fixed beginning with the Quartus II software version 10.1.