Well, first I’m not 100% this is a problem with the Beta 3 or if this sync is properly supported yet between both platforms.
The problem: I’m working mostly on-the-go and at home. To keep track of my deadlines I use both the calculate session word count by finish date and the option to omit do-not-compile parts from the overall word count.
I set them up in windows and would sync my documents via dropbox to iOS, work on my iPad on the go and then sync the documents back.
When I open the projects back on windows, the options to omit the do-not-compile is turned off again (I need to re-activate it for every project I synced.
Also, all deadline preferences are gone and I need to re-set every single one of them.
The only thing that is retained is the last daily word count that was calculated before closing the project and opening it on iOS.