before fully taking out the lino, I would first try removing just a small "cut out" (ie. just larger than the screw / bolt... size of a quarter or so) in an area that is the least visible. Use a sharp box cutter or equivalent. See what up with the underlying fastener. If you can tighten it down or whatever (ie. replace it with something better). Then glue the cutout back down. I suspect the fastener let loose from what it is screwed into or broke. Actually, what is likely is those fasteners weren't fully set to suck down the subfloor to the frame. Then with time and travel, the subfloor sat down leaving the fastener "proud" / high.
If that doesn't work, then you are likely left with removing the lino to address the issue although you might be able to "patch" with some "board like" equivalent pattern running accordingly.