Are these two sentences both correct? What is the different meaning between them?
1) The Karen had been sailing in a convoy to Russia WHEN she was torpedoed by an enemy submarine. (from a textbook)

2) The Karen was torpedoed by an enemy submarine WHEN she had been sailing in a convoy to Russia. (transformed by myself :)

Was the former 'when' used the same as the latter one?

Question

Are these two sentences both correct? What is the different meaning between them?
1) The Karen had been sailing in a convoy to Russia WHEN she was torpedoed by an enemy submarine. (from a textbook)

2)  The Karen was torpedoed by an enemy submarine WHEN she had been sailing in a convoy to Russia. (transformed by myself :)

Was the former 'when' used the same as the latter one?

Answer

We use the 'Past Perfect' clause - had been sailing - first because it's the first action and gives the reader the necessary background information. As a second clause we wouldn't use the past perfect but rather past continuous. 
"The Karen was torpedoed by an enemy submarine WHEN/WHILE she was sailing in a convoy to Russia." 
Past perfect is used for emphasis about what was happening, if that is not necessary than past continuous is better.
Hope that helps
Andrew