Is it possible to change scope while in a script?

There are situations within my organization's instances in which we need to clean up data that is spread out amongst multiple application scopes, and we find it very time consuming to manually switch between application scopes.

I had thought to have a fix script (or some other automation solution) to automate running through an encoded query of records to do things such as changing a bulk of update sets from complete to ignore. My question is: Is it possible to change application scope from within a scheduled job or fix script?

I've searched around docs and other community posts and haven't found an exact answer. 

Thank you!