Don't worry. The game keeps autosaves of ALL your playthroughs. You don't lose the old one, it's still there (with all the saves), you just get more saves for your latest path.
Now, important information for when Book 2 is released: which "path" it's going to continue from will depend on which path you finished last.
For example: say on October 25th you did Playthrough 1 (with choices x1,y1,z1) and finished the game, on October 27th you did Playthrough 2 and finished the game, and on November 5th you did a 3rd playthrough but only went half-way through (to see some dialogue choices you hadn't see) but stopped without finishing it, when Book 2 arrives it will use your Playthrough 2 choices to go forward. If you want, you can continue to Book 2 with your Playthrough 1 choices by LOADING the last save from that Playthrough and finishing the game, so now Playthrough 1 is the LATEST. (the same could be done with playthrough 3, 4, etc)
It is a little confusing (obviously), and we're talking to the devs in the forum if they can implement a clearer system before Book 2 comes out, but the important thing is:
YOUR PLAYTHROUGHS AREN'T ERASED, JUST NEW ONES ADDED
UNLESS YOU *FINISH* THE GAME WITH YOUR NEW PLAYTHROUGH, THE CHOICES YOU MADE WON'T CONTINUE IN THE NEXT BOOKS.
AKA, ONLY THE *LATEST* & *FINISHED* PLAYTHROUGH MATTERS FOR THE CONTINUATION.
(apologies for the Caps)