I'm not sure which option you are talking about. Do you have a screen shot of the option in RH11/10?
We have RH 2015. One of my team was moving folders around and didn't want to save the order when she exited. However, it saved it anyway and we thought it was tied to auto save. Turns out that moving folders takes place immediately and there is no un-doing.
First off, the option in RoboHelp 2015 is found here. File > Options > General section.
As for the folder arrangement, that's something you can turn off or on. Click the Project Manager pod and you should see a row of small icons at the top of the pod. One of the icons will govern whether files and folders are sorted as you want them to be in the pod (meaning you may click and drag to rearrange how they are listed) or whether they are simply listed as they would be in Windows Explorer (alphanumerically)