Is it possible to update one .mif file instead of the all set (to speed-up)

The command that executes the updating memory is quartus_cdb . Look at its description and details https://www.intel.com/content/dam/www/programmable/us/en/pdfs/literature/manual/tclscriptrefmnl.pdf, it doesn't have any argument specifically targeting to any ROM instance. It will update all memory blocks at once.