What you do is take the kinematic envelope measurements of the train and match it with the latest version of the infrastructure model. It is a computerised process that gives you an all clear or exceedances, down to the last mm. Then you deal with the exceedances, one by one. GWR are quite used to this.
Sometimes they are quite minor, like a speed sign being too close to the vehicle, or an under platform step needing a few mm shaved off, or a bonkers reading at a bridge, which is nearly always vegetation and easily dealt with. Sometimes you need to do a minor track slew, often where it has got out of adjustment with a platform.
Once you are all clear or can operate with restrictions, your class Statement of Compatibility can be updated and you are good to go. Eventually someone may update the SA but the SOC is now the important document to get right.