[whpalmer4]

First suggestion: OmniFocus queries might get more answers in the OmniFocus forum, not the OmniGraffle forum :-)

Second suggestion: contact the support ninjas tomorrow for help. 800-315-OMNI or +1-206-523-4152 or use Contact Omni in the gear menu in the iPad app. I can't quite figure out what is going on from your description, but I change dates all the time and have plenty of nesting in my project structure without any of the problems you are reporting while syncing. They should be able to get to the bottom of it with you.