Deleting activities on a baselined plan

I would leave them in the baseline thats teh whole point of having a baseline. If they have been deleted via a change notice you can put and actual start and finish date on those activites on the date that you were notified that they should be deleted. 

You can zero out the hours and reassigne the hours or you can add a deductive change

But if I zero out the hours on the current plan and put an actual start and finish date that will claim progress against the baseline plan for activities that weren't carried out? making it appear than progress has been made when it hasn't. Is that correct?

Keeping deleted activities is not best practice.  Dissolving activities is a shortcut that might induce errors if you do not verify logic.  A few years ago we had a job where one of the buildings was re-designed due to unforeseen conditions.  Footings, structure, architecture, electrical and everything else changed. 

For new Baseline best approach is to make updated version your new baseline.

http://www.planningplanet.com/blog/baseline-change-management

make the duration 0 days on those zero from zero is zero 

so you would rather say they were never part of the scope ? I would keep them and also in the activity description add the words (SCOPE DELTED) for each activity. the BASELINE NEVER GETS TOUCHED

why do you think that when you assign a basline to a project that it is no longer listed in the projects diectory ?

becasue that is done by design you do not alter an approved baseline 

https://www.rationalplan.com/projectmanagementblog/managing-projects-using-project-baselines/

• However, it is sometimes inevitable to adjust it due to a new requirement that implies a major change to scope or cost. Also in rare cases the project was not well scheduled since the initial phase. In these cases the best solution is to keep the initial baseline and to save the adjusted schedule as a new baseline. 

Frequently unforeseen events can be the cause of substantial re-alignment of the schedule.  Unforeseen events can be a hurricane or other weather event, change orders, Plans and/or Specifications Errors and Omissions, Owner Directed Change of Scope  (additions/deletions), Constructive Change, Consequential Change, Differing Site Conditions, and Jobsite Discovery of Hazardous Materials, to name a few, none of these due to poor planning by the contractor.  By the same token in these cases the best solution is to keep the initial baseline and to save the adjusted schedule as a new baseline.