Proteus copy sub-circuit
In case someone stumbles upon this old question, just like I did today.
In Proteus 8.XX both subcircuit symbol and schematics are copied to clipboard. You still have to reannotate the copies, though. Namely, you have to:

Change the references of newly copied subcircuits, so that they are unique;
Go to each child sheet, and execute global annotator for current branch or sheet (I found no difference, but my subcircuits are simple enough) with mode set to &quot;total&quot; (the mode being set to &quot;incremental&quot; is why it didn't work for you, probably).

The global annotator always accounts for all part referneces in the whole design, no matter what the scope is set to. The scope setting only defines what part of the design is to be reannotated.
Also, there's a good video explanation from Labcenter:
https://youtu.be/Cr-nB-LjbRI?t=54