OK Damir,
Each project has an identical structure. However, that doesn't mean that every project has to have a copy of each element. In fact, each unique element must appear only once in the entire (consolidated) repository.
Assuming that you agree with that assertion (and if you don't I really don't know how you can fix your problem) we have to refactor your current situation to achieve that.
Once we have a consolidated repository across all projects, we can create individual repositories for each project - each of which is a proper subset of the consolidated repository.
It would appear that your situation is more consistent than ours, but I'll still discuss the some project...
The first step is to create a new, blank repository.
Next you import each project into a separate root (as shown in the post above), stripping the GUIDs. The original GUID are no longer relevant.
You also need to create two additional projects:
Project Some and Project All. They have the same structure as the others, but initially NO content. You can import them in the same way.
Project A
- subordinate packages + diagrams + content (Classifiers)
Project B
- subordinate packages + diagrams + content (Classifiers)
Project C
- subordinate packages + diagrams + content (Classifiers)
Project Some
- subordinate packages (no diagrams or content)
Project All
- subordinate packages (no diagrams or content)
Now comes the hard bit... Pick one of your projects as the "primary" (if they aren't identical in content, pick the one with the most content). For the sake of the example, let's take Project B as the "primary".
For each content item (classifier) if the item is identically in all projects, move it from Project B to Project All (in the same part of the structure). Using the browser, you can move things in bulk, so it's not quite as cumbersome or onerous as it might first appear.
If the item is only in some of the other projects, move it to Project some (again, in the same structure).
if the item is only in project B, then leave it there.
At the end of this process, you have some things in Project All, some things in Project Some and the remainder in Project B.
All the diagrams, however, are still in project B. Their content will still be as before...
If you are OK so far, we can move onto the next step... If not, then we should stabilise this far first.
Paolo