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I would think it refers to the author's main Vajrayana teacher. As ChrisW rightly notes: Thunderbolt is a translation of Vajra. the lord The student-teacher relationship is very important in Buddhist tantra and Santideva was an Indian practitioner of Buddhist tantra.
There are several reasons to think that it refers to his personal teacher: 1) in tantra one is supposed to see the teacher as one with the highest Buddha 2) in the text here it says that the author has neglected 'his instructions' - that is, the instructions of the Lord of the Thunderbolt. That makes most sense if it does refer to his personal teacher.