Sentence 2 means that you have employees other than Jane, Tom, Pete, and Harry, and that the documents of those other employees were not stolen. It says nothing about whether ALL of the documentation of the four is missing, or merely some of it.
Sentence 1 is unclear, because "some" could refer to either employees or documents.
Here are the clear possibilities:
All documents of some of our employees were stolen. (Or: Some of our employees had all their documents stolen.)
All documents of all our employees were stolen (Or: All our employee documentation was stolen.)
All our employees had some of their documents stolen.
Some of our employees had some documents stolen.