'save set' should store 'unset object' before saving the current objects. To illustrate this:
set object 1 rectangle from screen 0.4,0.4 to 0.6,0.6
save set 'blubb.gp'
set object 2 rectangle from screen 0.5,0.5 to 0.7,0.7
load set 'blubb.gp'
plot x # shows both objects
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