What's this negative pressure on drain side??
As stated above, it's a U-bend trap with water lying in the base of the U.
The water will be at the same level on both sides of the trap when the air pressures are the same on both sides.
If the pressure is higher on the drain side, then the water level will be pushed down on the drain side and will rise on the house side until the water seal is broken and bubbles of sewer gas will enter the house. This is what was happening previously and it suggests there may be a blockage. The gas should be vented from the top of a soil and vent (S&V)pipe. It could happen if the original S&V pipes had been removed and air admittance valves installed.
If the pressure is lower (negative, less than atmospheric pressure) on the drain side, the water level will be sucked up on the drain side and will be lower on the house side. This is what is happening now and guess what it may indicate? It suggests there may be a blockage since the drains should be vented through a S&V pipe so that they are always at atmospheric pressure.
I'd have expected the toilet U-band level to revert to normal after flushing with the manhole open, since that would allow air into the drains.
It might also happen if you've installed a FOGB ventilation plant and your house is at positive pressure. I think you might have noticed that though.
I'd suggest you find your S&V pipe and check for blockages ( or the S&V pipe having been removed or amended, e.g., during a loft conversion) between the toilet connection and the top of the S&V pipe.
PS Another thought; the rainwater drains are usually(but not always) separate from the foul drains, since the rain water will usually discharge into a nearby stream. If the toilet is an alteration, it might be wrongly connected to the rain water drains. That could explain why the rain caused a change in level and why there's no ventilation into the drains.