I am importing a very large Scrivener Project from a MAC to the PC Version and lose many of the files-- or at least they do not appear on the left navigation panel after synching the files (Via Goodsynch).
It seems to be a bug but perhaps there is something I do not know about.
I have no experience with GoodSync, nor any reports on whether it works with Scrivener or not. The key thing it needs to do is keep every file in the project up to date at all times. It sounds like it might not be updating the Binder .scrivx file correctly, if there are missing outline elements. Definitely produce zipped backup copies at the end of each session alongside the .scriv folder. If the .scriv folder malfunctions, you can then remove it and unzip the latest backup copy.