This is quite weird that such a limitation exists. This is wrong, IMO.
To reproduce:

• have a dummy template with 2 dummy items, both placed on a graph;
• link the template to a dummy host;
• unlink the template from the host;
• edit the host graph and remove one of the items from it;
• try to link the template back to the host, to restore all its settings on a host;
  You got the error:

  Graph "TestG" already exists on "TestH" (items are not identical). 
  

This is strange, because if I do more significant and more affecting changes on existing objects on the host, like:

• changing any item's settings,
• changing any trigger's settings (including dependencies),
• deleting any objects,
  they will be re-created and all differences will be forcibly overwritten from the template.

So, question arises - why graphs are so different to be "against" my desire to re-apply everything from template?
I really want that items on graph would be added and the template being successfully linked!

 This is a real life scenario, when templates being prepared/tuned on a Test env and then being exported to be imported on Prod env. And it appears to be not allowed ...
I believe this should be revisited and allowed.