If almost a meter is to be filled up, heavy equipment will be on site anyway. dig out, fill up one meter and reset the cistern.
However, the inflow and outflow will no longer match in height and must also be relaid, if this is at all so easily possible considering the slope, etc...
Whereas processes are the smaller problem. With rainwater, the slope is quite irrelevant, if necessary you make a drop to the old sewer. Inlets would actually have to be newly laid. Although there should then also be enough height potential, it is just work to dig everything up again without destroying half of the pipes
However, the supply and discharge no longer match the heights and must also be re-laid, if this is even possible so easily considering the slope, etc....
And that is exactly why it would be sensible to include everything in the question right away and not have to extract everything from thin air.
Possibly leave the cistern as it is; compensate for the planned terrain with (significantly) larger concrete rings than the shaft without connection to the cistern. This way you would also have no problems later accessing the filter and so on.