Steve,
There are still some issues with OpenToonz saving that (as near as I can tell) has a little to do with root directories but also with saving of scene files. This should be resolved soon and as near as I can tell is working as expected in the most recent release of Motion Monster which incorporates a few cutting edge additions that haven't made their way into the official release of OpenToonz yet.
I won't get this quite right... because I can't account for all the variables.. BUT... before using Save All in OpenToonz I almost always save the scene first. This process would appear to be what is going to happen when Save All is launched but that isn't always the case. A key to success is to first create a Project... then a Scene... saving the Scene then keeps things in order. It's that nebulus ares between Project and unsaved Scenes that occasionally results in missing resources. The resource is usually there but the links don't point to their proper location.
This issue isn't related to PSD files/format but occurs anytime a link doesn't point to a proper location.
Think of it in a similar what to webpages... where an html hyperlink points to another page (or image) but generates a broken link if the resource at that location has been moved to another location. The two options we have is to put the resource back into it's proper location (where the link points to) or to edit the link to point to the new location.
As I said, the most current release of Motion Monster addresses this issue in an interesting way. Namely, it emphasizes that we should create a Project location first and then use Scenes located inside those Project locations.
One thing that will help as well (even with the new popup that emphasizes Project and Scene) is that immediately after creating a new Scene we should save that Scene. Saving the Scene ensures that the link between the Scene and Project location is established whereas if we don't save it we run the risk of the link... or the resource at the end of the link... going away.