I think to be as explicitly accurate as the manual is, you should activate the Indian Ocean files only when you will end your patrol in Indian Waters.
If you have been transferred to Penang but you'll be sailing out of a French port and going there yourself then you activate the files.
If you are sailing from Penang on patrol and expect to end your patrol in Penang then keep the files active.
If you are sailing from Penang to France and will end your patrol in a French or other European port then disable them.
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