I don’t delete unused data or anything like that until I am finished with the project. I just copy the project files and contents to a second drive. ‘Prepare Archive’ just copies any files into the project folder that maybe stored elsewhere. That should be done if you haven’t set your preference to copy files on import to project.
Then I work on daily with the original project folder and repeat at the end of each day, replacing the folder on the backup drive
Before archiving the finished project, I either:
Prepare Archive, Remove Unused Media, Empty Trash (in that order)
These processes minimise the project size by deleting unused and unreferenced files
Also be careful to note that some VSTi s reference their samples to a specific location (Battery for example). In order to make your project completely reliable for the future, you may have to save those samples to within your project folder, or, on re-opening (on a different system for example) those samples would be missing. Each VSTi has it’s own way of doing this.
I guess it’s best if you use a test project and work out a routine that works best for you.
ps. My hard lesson was learned when my main audio drive failed one morning - disappeared from Windows and Bios forever. I lost six current album projects and a lot of sleep. Finally the contents of the drive were recovered by a specialist company. It cost over £700, but worth it as losing all that data in front of clients would have been just too awful. Now, I take the time to backup!!