Issues around safety and ventilation in those tunnels iirc.
The only safety hazards are the 400kv cables currently plonked through the tunnels, they were only built in the 20th century and ventilation wasn’t an issue because they were intended for operation by electric traction. Considering the Sheffield end is likely to be electrified towards London sooner rather than later the ventilation argument becomes increasingly null & void. In any case, ventilation is already an issue on the existing rail route through Totley tunnel.
Rail isn’t really suitable for short trips like Sheffield to Manchester + there is already a rail line between the cities. It’s naive to think that a single trip would be saved if there was more freight capacity on the route.
Of course it is, two large university cities less than 40 miles but the best part of 90 minutes apart by road?
The current rail route is circuitous and takes an hour which is nearly as bad as the road journey, and is also operating at full capacity having to make allowances for slow stopping trains and freight services to and from Peak Forest.