Yes, the GUID is unfortunately different and the only way to solve this problem would be by finding the equivalent reference of a GO from one scene to another.
Starting with looking at names or hierarchy. But the name method is limited because of many GOs using the same name, and even the hierarchy solution would be hazardous although more accurate because it would use the path access to find where the GO is in the hierarchy, but then would hit a wall if it found a parent to host several children with the same name and no particular order, unless it took into consideration the GO's position in said local hierarchy, at this level. That is, having 40 "shoe" GOs under the same parent for example is not going to help unless their order is taken into account.
So basically, in this case the solution is to go through them one by one and update each reference manually.