A few years ago I was involved in a job where because of unforeseen underground conditions a building had to be replaced with another building whose design was radically different.  Almost everything changed; no longer spread footings but pile foundations, wall materials and layout changed, structural design changed, links to site work activities changed, the construction sequence of the project as a whole changed.  Keeping hundreds of the no longer valid activities would be insanely ridiculous.

I had prior personal experience with GAO, enough to know they are not as respectable as some people claim.  I was bidding as a subcontractor for a Federal job where P6 was brand name specified something that is unlawful under federal laws unless on a case by case basis a waiver is requested and approved, perhaps after a dubious review process.  I was ruled out of this bid as I use software different to P6.   When I issued a claim GAO simply called me without standing and never took action as to enforce their own dummy requirements.  GAO is a government agency that responds to political interests, their action/inaction affects many outside government agencies.  Reasoning with GAO is a waste of time.

I suggest its advocates just prove my arguments are wrong using valid reasoning instead of making superfluous arguments.

I suggest start with the very first reason why GAO is wrong – “If the activity is no longer valid, its duration should be zeroed out and the activity marked as complete”.

Keeping deleted activities as well as leaving the original logic in place is not best practice:

• Keeping deleted activities can be confusing and misleading. Changed conditions might require hundreds of activities to be deleted and can create chaos if not deleted on revised schedule.
• Keeping deleted activities can distort cost loading if you if you miss to delete some cost assignments.
• Keeping deleted activities can lead to wrong schedule logic when there are still some active links to activities that no longer exists, mere change in activity duration do not tackle this issue.
• If you keep "deleted" activities project statistics such as number of activities and other ratios will become meaningless. 

One exception to this rule should be good enough to make it not reliable.  I provided not only one but several/many reasons why this rule is not best practice, in any case worst practice.