Sorry for the problem you experienced.
I think you have done one of below steps:
A. delete user story, reopen project without save.
B. deleted/renamed vux file next to your vpp (or moved vpp file to another location without vux file)
User story data is save immediately.
In other words, even not saving project, user story data are already saved.
User story data is stored in this file (or VPository or VPServer).
If this file lost, all created user stories will identify as deleted.