Nested embedded and linked blocks disappear all of a sudden and get replaced with nested block

Hi there,
I have a rather odd problem I am not even sure I will be able to describe properly here.
(Please do not be too confused…)

The thing is that we are using linked and embedded blocks in our projects.
And of course it’s gonna happen that we gonna have nested blocks that all contain linked blocks.

So I was designing stuff on my desktop (of course) and referencing files into other files as blocks.
My idea was, that once we gonna move that stuff on the server I’d be able to simply change the paths via scripting and we’d gonna be able to update them.

The result was a very odd one:
Some (really only a few) of the superior blocks (containing the nested blocks) vanished and at the location (and orientation) of theirs I found a single block (part of the nested ones) and no trace leading back to it’s initial superior block.

This description is very poor and I cannot reconstruct it here, because in my eyes that is not possible.
We also had very long and extensive discussions in our team and we did come to the conclusion that it must have been a very unlucky accident? (Or let’s say we rather hope that it is).

So the questions I have are:

  • Did anyone experience a similar situation?
  • What are the best strategies for linked and embedded blocks?
  • Is the way we work a good way to work after all?
  • How can one avoid a bad awakening like ours?

Thanks for your feedback in advance…