I have been mainly using the desktop to avoid this issue, however, would love to be able to use the two formats together if I trusted it would work. The iPad version will often lock up on me after downloading new info from dropbox. I have to shutdown the iPad and restart it to get it to open, or sometimes just leaving it and coming back much later (not sure how long I usually wait a good hour or more before trying again) will work as well. This works to keep the info on the iPad up to date, but I have not until yesterday, been doing work on the iPad version to sync back to the desktop.
I just did this yesterday and now dropbox is telling me there is a discrepancy in the files (can't remember the wording and the message box is gone now). I updated info in the iPad and uploaded it to dropbox. None of the changes transferred to the desktop, so I did it all again on the desktop instead. I uploaded the changes and downloaded to the iPad (which did not lock up - there seems to be no rhyme or reason to when it will or won't lock up). This morning was when I got the message of the error. I have a first generation iPad (not sure if that is part of the issue either). And since the changes transferred I don't know if this is anything I need to be concerned with (or if it may be part of why I can't transfer changes from the iPad to the desktop?) Thanks!