When you convert an existing MPLAB IDE v8 project to the new MPLAB X IDE format, you will have the ability to share the project between both versions of the IDE. The conversion process makes no changes to the version 8 project except to add a new directory inside the project directory with the name v8ProjectName.X where v8ProjectName is the name of your version 8 project. This new directory will contain all of the MPLAB X IDE project files, but the project will point to the source files of the version 8 project. This arrangement means that the MPLAB X IDE files will not "pollute" your MPLAB IDE v8 project's directory. This also means that both projects share the same source files, allowing you to work on them from within either version of the IDE. However, all the project settings from this point forward are separate. So, if you change a compiler optimization setting in one project, it will not automatically change in the other.
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