[HELP] Duplicating a parent sequence so that all nested sequences within it are also duplicated and in not way linked to their originals

As Chris stated, concerning the 'Pancake' workflow with another project version saved for editing,

you can easily and seamlessly drag and drop from one project's timeline to the other, or you can also

drag nested sequences from the timeline to the project panel, that which creates duplicates of those

sequences, but make sure to drag other nested sequences inside that sequence in order to make

unique duplicates of them. You can also right click the nested sequence from the project panel and

choose 'Duplicate', but the 'pancake' stacked workflow is easier as you can see more clearly and

work seamlessly.. needs a bit of practice...

Make 2 versions of that project template, the master project that you leave intact, and the editing project,

open both projects in Premiere Pro, stack the export edit (or final edit) sequence of the template under the

main sequence of your new project, and start dragging from the export edit template sequence to your new

sequence, this will create unique duplicates of everything. For added duplicates, simply drag nested sequences

from the template timeline to your new sequence Project Panel...

Hope this helps

Unfortunately You can't. Actually it's more like fortunately as the ability to do this will cause chaos.
The best practice is that when you duplicate the sequence, duplicate the nested sequences that you are editing, it's only a couple of clicks away, and gives you the opportunity to rename.

Alternatively, you can create a new project, and duplicate the main sequence to it, do your edits of the nested sequences in the new project. After editing, you can copy back the main sequence to the original project, and by doing so, PP will duplicate only the nested sequences where an edit has been done. what you can do to make your life even easier, is to use a pancake workflow. In case you are not aware, PP allows you to open multiple projects in one instance

If you need further explanation, please let me know.