I would recommend looking at how you will implement the training as well.
Will new employees be cross trained to be able to work at both locations? Or will they be trained to only work at one location?
If they are to be trained for both locations, it may be beneficial to keep one set of documents and specify the differences within the documents.
My previous experience is in the pharmaceutical industry and where I worked we had 4 different packaging lines. As many of the functions were the same, but there were minor changes, these variances were called out in the same SOP or on the job training document. Each of the packaging lines were assigned a different colour and so that section specific for that line would have a bolded statement at the beginning of the paragraph with the associated colour. The colours were also posted on the lines, and specific tools only used for that line were colour coded with tape or shrink wrap so it was ingrained across the board. For example, it could be like this
General instructions for both sites here blah blah blah...,...
FOR SITE 2 ONLY - ensure that the switch is placed in the on position before starting the mixing process
continue with general instructions......
You could also do something like the following
FOR SITE 2 refer to SOP-2-2100 (with the 2 representing site 2) for mixing process set-up procedure
Both allow you to call out the difference in procedure but if your general processes are the same, this reduces unnecessary documentation.
Overall, learn your processes and know the DIFFERENCES between the sites. If they are essentially the same, don't make work and duplicate everything since going through and making major updates will take more time to have to update the same document effective at the two different sites. If there is a procedure that is vastly different or not even applicable at one of the sites, pull that document out, assign a site specific code and make it its own document.
I have learned the more redundancy you have in a documentation system, the more work you make for yourself and the team if that process has to be changed across multiple documents. You are more likely to miss a reference and increase employee confusion and potential NCs.
GOOD LUCK tackling this and do what works best for your sites & employees. Ask management and the employees USING the documents so you can get the buy in you need to support you in this transition!!