If you're not modifying the Hardware Design and only modifying the SW BSP and application in a NIOS II design, you need not recompile the whole HW / Qsys part. You only need re-compile the SW Eclipse BSP and application.
On the other hand, if you modify the HW design via QSYS, you will have to compile the entire HW platform using Quartus and then regenerate the BSP and Application using Eclpise. This is because a change in HW platform invalidates the BSP and Application.
