It is very sensitive politically. There could be riots over fare rise. Precisely for this reason, these special fare special trains are deployed. IMO, these should be accorded good priority for their runs since they are actually charging premium trains' equivalent or more fare.
To cut running expenses, railways should cut some posts altogether. Like peons, sweepers, coolies (who carry guards' trunks), etc. Such non-skilled jobs not just give quarters, but very high salaries (thanks to pay commissions), free medical, handsome pensions, free travel, etc. Who knows next couple of Pay Commissions would propel their salaries above 1 Lakh Rupees per month! Isn't that criminal waste of taxpayers' money?