Audit scope

Changing the scope of your quality management system is can be done, even between the stage 1 and stage 2 audits, but requires discussion with your certification body before you do so and may incur some additional changes as they may need to repeat the sage 1 audit to the new scope. The big question is this; considering your scope is basically where you have identified the rules of your QMS to be applicable, why are you changing it just to make things easier. Since this is where the QMS rules need to be applied, then this change requires some thought because you are basically stating that you made a mistake with your first assessment of what should be included, and now you need to include less of your company.

You can find out more about writing the scope of the QMS in this 9001academy article: How to define the scope of the QMS according to ISO 9001:2015, https://advisera.com/9001academy/knowledgebase/how-to-define-the-scope-of-the-qms-according-to-iso-90012015/

If you need some help organizing your implementation, you may find out book helpful: Applying AS9100 Rev D, https://advisera.com/books/applying-as9100-rev-d/

The reason for the original questions stems from the material that we produce.  The line that we want to focus the AS9100 audit scheme on is for the Aerospace industry.  We only make aerospace items on this one line.  The other equipment will be kepr under the ISO scope

Having AS9100 scope for one aerospace product line and ISO 9001 scope for other parts of your organization is an acceptable thing to do, and I understand why you would want to do so. Just ensure you talk to your certification body about the scope change.