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one way I would suggest:

1. save your original project/session as an archive/zip (*.qtz file extension suffix); that would bundle all stuff in a bundle for safe and archival purposes;
2. then you can duplicate it (Save As... again) into another working project/session, possibly to another-name.qtz file to serve as baseline;
3. after making this new baseline.qtz file, it probably makes sense to now save it again as a regular non-archive/zip file. with the *.qtr suffix back again as usual but now you get a brand new base session directory as a working copy of everything from the original session.

get the idea?