The only exception is when loft insulation is topped up to current regs i.e. way way way above the tops of joists. In these cases, it is better for the junction boxes to rest on the top of the insulation so that they are accessible for inspection. The same for cables too - although if they are clipped correctly to joists, they are OK.
If re-wiring in the loft with knee deep insulation, it's best to leave the cable on top, following an approx. joist run with some slack in case the loft insulation needs to be moved for whatever reason. Or fix battens to the rafters to clip the cable too and use a bit of plastic drainpipe above the light fittings to provide a cable route and serve as a marker for the future.
Gary, it depends on how much you are prepared to degrade the insulation by trampling on it, ripping it, tearing it etc. I agree with you regarding battens and rafters, but I have been on jobs before that:
a. have been too risky to gain access to certain parts of the loft due to knee deep insulation i.e. right in the edges, awkward trussed roofs etc.
b. would have degraded the loft insulation to such a point that Part L would be compromised and notifcation would not be possible
c. would have taken weeks to complete
In some cases, leaving the cables on top of knee deep insulation keeps them visible. And this can be much the lesser of two evils.
Knee deep insulation renders the loft inaccessible for 'normal' loft useage i.e. emergency access only. Therefore I don't see it as a risk factor to have cables lying on top of knee deep insulation. If the cable has sufficient slack, it can be lifted for the temporary insertion of loft boards should access be required in the future.
Junction boxes should be screwed to a short batten/floor board with the cables clipped to avoid stress on the connections should it be moved in the future.
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