Audacity projects have a matching AUP file and a _DATA folder. The AUP file is the show manager and tells Audacity how to use the work inside the _DATA folder. Sometimes you can save a damaged simple recording with the recovery tools and without the AUP file.
My immediate reaction on reading that statement was: oh yes it will! I use v2.0.2 and, when assembling a soundtrack, regularly do File > Save Project. Audacity always overwrites what was previously there, and I do not receive any warning message. Please note: I understand the risks of working this way and accept those risks. So, could you please clarify what you meant by that statement?