No, they are not permanent.
The saves are located in C:\Users\<Your Name>\AppData\Roaming\RenPy\DreamsofDesire-bunchofnumbers. Delete the files inside of there, and you'll be fresh. That's how it is on Windows, anyways; can't answer about other OSes.
Maybe I'm using mine differently than I should I have all my d/l games on a 2nd hard drive, different from the o/s or that I use UnRen and they also store in a save folder within the game folder
F:\DreamsOfDesireEP10-ELITE-100-pc-Skunked\DreamsOfDesireEP10-ELITE-1.0.0-pc-Skunked\game\saves
the naming within the saves folder is fairly self evident when you look at it too.
All of my RenPy games store saves like this - gonna have to experiment with deleting from one and not the other....but so far coping the saves from the game folder has worked ok for me.
ETA
A quick experiment and changing the name of the save folder in \game:
it creates a new 'save' folder but pulls up the saves from AppData
Changing the name of one of the saves in \game\save to move it's postion 2-1 to 3-1 it then pulls up the 2-1 save from AppData and slots that in.
Not such a bad thing as your saves are backed up but it is duplicating leaving me with 112Mb of saves in AppData that I don't really need (other than the day everything goes to shit and I need the back ups).