The revenue for the railways isn't calculated like that.
For example, if NMPT pays the railways 1 Crore (just a random number for illustration) for a full coal rake from NMPT to SBC, then the revenue is split like this -
1) A small fraction (usually 5% for passenger trains, I don't the know the exact number though) - roughly 5% will be set aside for the zone handling the loading, in this case 5 lakhs for SR.
2)...
more... The remaining the 95 lakhs will be split in the ratio of the distance traveled by the train in each zone. In this case, roughly 15km in SR and 350km in SWR. So, SWR gets about 90 lakhs and SR gets about 5 lakhs.
But if the train is going from NMPT to any destination in SR, then the entire 1 crore will be given to SR.
So, as you can see, in most cases, the fraction of the revenue that SR gets because of 'NMPT being located in their jurisdiction' is very less. (5 -10 lakhs vs the full revenue). So, out of the 385 crore revenue you mentioned, more than 80% would be revenue due to the train 'running on SR tracks', and some part of the remaining 20% would be due to 'NMPT being present in SR'.
If the section is transferred to SWR or KR, then SR will only be losing a part of that remaining 20%.