I had my NCS appointment today, applying on the basis of being married to a BC (went down EEA3 route first to get my "document certifying permanent residence"). The lady wanted proof of 5 years' residency (luckily I'd brought 5 years' worth of documents just in case even though 3 should have been enough - am I correct?) and said they accepted only P60s, SA statements of account for the self-employed or benefit letters. I'm self-employed but have no statements for two of the five years as I didn't owe anything and consequently HMRC didn't send me statements (they are numbered sequentially so it's clear that there are none missing). Based on what I had read on this forum I brought along the SA statements I have, council tax bills, water bills, a letter from HMRC, a letter about jury service etc. She said none of these would be accepted but agreed to send everything anyway. She was also talking about treaty rights however... This whole EEA thing just seems too confusing for everyone!
Anyway, just wanted to say you should be fine with your P60s. Just send them again, who cares if they should technically be asking for them or not as long as you get your approval.