I have had my roof retiled, etc in the past 18 months and probably a third of the properties around here have in the past couple of years, by all different roofers. I can tell you now that not a single one has had a building certificate - none of the home owners or roofers themselves will even be aware of it. Nobody cares and it's never likely to be an issue. I've never heard of this coming up when selling but in the highly unlikely event that it did just say you're not sure when it was done and have photos of your well insulated loft (which you can do at any time and is the reason for this stupid, intrusive requirement) - OR: you simply get some insurance costing about 80 quid to cover possible regulatory issues for the buyer; your conveyancor will know all about it. This is common where possible covenant and consent issues are unclear and it happens all the time.
The roof is still classed as the thermal element, whether the insulation is at joist or rafter level. If you want to add insulation at joist level, the easiest time is when the roof has been stripped.
Most of the roofers I know are part of the Competent roofers scheme, so will self certify at the end of the job.
It's right that it's unlikely that the council will ever take enforcement action, and unlikely a surveyor will pick it up on a house sale, as a roof soon alters from it's brand new look.
However, the advantage of having it signed off for a house sale is that you can tell the buyers it's a year old roof, hopefully with an insurance backed warranty.
Also, if you've only got 100mm of old fibreglass in the loft, this is the easiest time to bump it up, as the roof is the biggest heat loss.
TBH I thought it was 25% of the roof until last year when I job I was doing involved Building Control on some drainage work and the customer asked me about some roof repairs. I said to the BCO, that it looked like around 25% to me.
He said 25% causes too many issues working when doing repairs trying to work it out, whereas 50% virtually means when a complete new roof is done.
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