I checked the source (gstrtpjitterbuffer.c) and the GstRTPPacketLost event indeed contains the seqnum!
gst_structure_new ("GstRTPPacketLost",
"seqnum", G_TYPE_UINT, (guint) next_seqnum,
"timestamp", G_TYPE_UINT64, out_time,
"duration", G_TYPE_UINT64, duration, NULL));