Too many people making assumptions about clearances. It's one area that grandfather rights very often won't apply thanks to re-alignments suited to current traction, not that of yesteryear.
I think you are one of them. If it says in the Sectional Appendix that a line is to be clear for a certain type of train, the line legally has to be kept clear for that type of train full stop. Unless a change is agreed between all the relevant TOC's and FOC's and Network Rail.
Any re-alignments should normally be designed to at least maintain existing clearances, and any low hanging improvements grabbed. As any extra clearance adds to the safety margin and allows the maintainers more to play with before they get told that they can not tamp that location again, as the clearances are at the limit. There should also be up to date site recorded data on the clearances at each structure as the track can creep sideways over time and maintenance activity tends to lift it. If you do not know what your clearances are you run a constant risk that one day a train loaded a bit more than normal, on a slightly softer suspension will take a puff of wind etc etc at just the wrong time and there will be a rather loud bang.
There is data for most train types that quantifies how big an area or kinematic envelope a train can fill for any given curve and speed. Basically the maximum height and width the train could reach if it bounced, canted and curved the maximum amount in every direction on the spot.
It should then be simply a matter of comparing the composite worst structure gauge with the maximum kinematic envelope. If the kinematic envelope fits through the composite worst structure great no problem.
If it does not you then have to do a more detailed analyses. To prove if the areas where the two lines overlap are co-incident on the ground, as the tighter structural clearances, may be at a places where the train will be at a slow speed and hence bouncing less giving a smaller kinematic envelope, and being on the straight not using that part of the kinematic envelope caused by end and side throw. There are computer programs that will run the kinematic envelope for a train along a line adjusting its size for the line speed, cant and curvature etc checking the relevant envelope against the structure gauge at the same point. This is a lot of computing and takes time, the result then needs to be sense checked by a gauging engineer of which there are not many. With any conflicts investigated to see if they are real, or if the laser on the structure gauging train just recorded an overhanging weed or some litter blown by the train.
The question is why did this problem only emerge so late, does Network Rail not have enough Gauging Engineers, or did one of them just forget to promptly action the checks or even a bit of both. As the need for a gauging check should have been flagged up the moment someone asked to run stock not listed in the Sectional Appendix.