Something doesn't add up here. Initially the OP was saying "as the extension will be over the top of the existing sewer manhole" They then went on to say the sewer is about 2 m deep and the builder had dug a trench from the manhole in an attempt to trace the drain run. Why not just look down the manhole? Are you getter "sewer" and "drain" mixed up by any chance?
The latest revelation that the sewer is in fact 5 metres deep is extremely unusual. Unless it is a main trunk sewer why on earth would they put it 5 metres underground, that makes no sense. Exactly how was that depth established and why did it take so long to find this out if there was a manhole on the sewer the whole time?
In my dealings with the water companies I find that their information on the location and depth of sewers is extremely sketchy, they have only a vague idea of roughly where they run and how deep. When you make your build over application it is therefore preferable to have already confirmed the exact position and depth of the sewer so you are not at the mercy of their vague and haphazard assumptions.
Ok to answer the above, we was totally unaware of the sewer location, again I'm not a specialist in these matters, to me the manhole is the sewer, however now I know a bit more I can provide some clarity.
We have a rear extension that sticks out roughly 4m and is approx 3m wide, to the side of this around 200mm is the manhole, this manhole has a pipe that connects down to the sewer main which is approx 5m deep and 1.9m from the rear of the extension into the garden.
I now know all of this as we have had a CCTV and Sonde survey done and they have mapped the sewer for us, as you say SW records are extremely sketchy, their plan shows the sewer main actually under our extension where as in reality it's almost 2m away from it.
SW refuse the build over as the sewer is deemed Critical by depth as it's approx 5m deep, and your not allowed to build within 3m of that.
So we are trying to assess our options, someone has mentioned piling, my other option is to bring the extension on the side back by 1.1m so I'm on the edge of their 3m rule and thus dont need a build over agreement I believe?
Additionally to this I can also build on the other side of the extension as it's less than 3m as permitted development to get back some of the space I will be losing by not being able to go with the original plan.
The only question I really now have for SW is if I can remove the manhole completely, join our new waste to the existing connection with a rubber sleeve and put a rodding point in for access, thats the only question they are avoiding totally right now as they are fixated with this critical main sewer and wanting me to stump up tens of thousands to divert it.
The whole thing is a mess and a nightmare, and it's dragging on and on, Im at the point I just want a solid decision so I can adjust our plans accordingly