Is there a way to combine sof and elf files ?

out of my head i remember that there was an issue with the filename for memory initialisation.

if i am right the default name given for this file is recomended to be changed to a user choosen filename. like myOnChipMem.MIF

also i have seen a couple times that quartus modifies MIF and HEX until they were set to read only.

in some other cases only a MIF was producing a new sof, even if the hex file was correctly entered

i know this is woodoo but try to choose a fileename you created, check that the files produced by sopc / wizzard & co have this filename and it is located within the root of your project.

your memory source file should have an entry like

altsyncram_component.init_file = "My_Memory_Init.mif",

your memory does not need to be RAM it can be ROM for nios instruction data.

one last comment, i had this pitfall a couple of times when i haven't noticed that quartus wasn't creating a non time limited sof like usually. the licence server was down and quartus created a sof with a different file name _time_limited or so added. my quartus programmer and all comandline batches were trying to update the (not modified) sof.

so check your project if you have more then sof or if your sof is realy updated