Thanks guys, Yes it is confusing first time round - all new to me.
From reading the wiring guide - closest example of our current setup for 2240-4 would be on page 43 ( although it is for a 2050 series - but the wiring guide is universal )
https://library.netapp.com/ecm/ecm_get_file/ECMM1280392
FAS2050 multipath HA configuration with one disk shelf
The SAS port cabling sequence for each controller is 1a,1b.

When I copy the cable wiring to our current FAS2240-4, following the circle > square relationship. it would look like below.

Which is also the same as the FAS2240-2 with external shelf,

and also same as
Top Controller (A) Circle port connects to Shelf 1 Top (A) module Square port
Bottom Controller (B) Circle port connects to Shelf 1 Bottom (B) Square port
Shelf 1 Top (A) module circle port connects to Bottom Controller (B) Square port
Shelf 1 Bottom (B) module circle port connects to Top Controller (A) Square port
Now the fun part of correcting this - without effecting current production systems on the filer.