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Do you have backups enabled like Curt mentioned above ?
I've never used the welcome template myself so I'm wondering if that has anything to do with it ?

First go to " omni focus " then preferences then the general tab and check your backup prefs ...

If you're set to backup I'm wondering if the welcome template is trashing data somehow ? or is your data in another open window ?
If you click on " window " in the menu bar , how many show as open ?