"Hazel and I had had a couple of holidays in Agastri and had made some Greek friends there."
why "The Past Perfect Tense" is used in this sentence?
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The speaker is presumably setting these past events clearly into a previous time frame. There is no way of fully assessing this use without the surrounding context, however.
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On the contrary, the simple past appears as 'we travelled'. Because of the 'before' in the first clause, the past perfect is not necessary here, but the writer wishes to make clear that they had already travelled in the region previously. The past perfect here stresses that.
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