PROCTools: More improvements to update references script

In !62281 (merged) I realised that the script didn't support:

• simultaneous digest and pool changes in one MR
• multi-line diff changes

This MR significantly simplifies diff handling (using the fact that event/run is a unique identifier and so we don't need more than this to identify which line to change) and now supports both of the above

cc @atlas-release-coordinators