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;
then you can duplicate it (Save As... again) into another working project/session, possibly to another-name.qtz file to serve as baseline;
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.
one way I would suggest:
get the idea?