Quartus version 184.108.40.206
We have not made any changes to the design but are just rebuilding, QP V16.1 is a new download on a new PC, but the identical version to the original build.
Design is a Cyclone V with a HPS core. A number of the files in the hps_isw_handoff\QsysProject_hps_0 folder are different in the new build - they have a later copyright date, e.g. 2016 Intel in new and 2012 Altera in original build.
The software has changed quite a bit in 4 years. As you noticed, the handoff files are different as well. You'll need to rebuild the preloader (now usually referred to as the first stage bootloader).