Just don't lock any methods...
For instance, I use a lot of instrument methods for GC, HPLC and UPLC, with different detectors and settings etc. So if I need to change my wavelength resolution from 4.8 to 2.4 etc or add channels, change temperature, as long as you have Full Audit Trail enabled in your Empower system policies, you have to provide a comment when making each change. This comment is visible in the audit trail connected to that method.
You can always see what method parameters are connected to each run, so if any changes occur between runs, they can be viewed under method properties. If you want to go deeper you can "View Differences" between two versions of a method to show an auditor exactly what was changed (but the "why" it was changed should be an audit friendly answer!).
I can kind of understand locking down instrument methods in a highly regulated QC lab with one active peak that doesn't ever change Retention Time or Assay from one end of the year to the other but locking processing methods is madness in my view- stability samples stored at different timepoints and temperatures are extremely prone to variable behaviour in terms of peak shape, degradation profiles etc and the analyst needs the freedom to use any and all of the Empower features to aid integration of the sample at hand.