I just submitted the below via Send Feedback. However, I wanted to register and post it here also because I was a very bad beta tester and did not give Omni enough useful information to reproduce the problem.

(I was a particularly bad beta tester because I have gotten so used to OmniFocus reliability that I actually put some data in there and deleted the originals. Naughty! Naughty!)

Has anyone else seen a problem like this and come up with a way to reproduce it? It's obviously pretty serious and unlike anything else that's happened to me while using OmniFocus.

I also will work on reproducing it once I finish beating myself up over the lost data. :-(

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In the latest beta, I added a bunch of items and then tried to organize
them into hierarchical projects in the Library.

I created a top-level project ("Group") to contain three related
projects. I renamed them to get rid of the redundant bit and dragged
them inside it.

"Group Item1" -> "Group" / "Item1"
"Group Item2" -> "Group" / "Item2"
"Group Item3" -> "Group" / "Item3"

With the top-level "Group" library folder open, I attempted to drag a
task from that folder into another task ("Item1") to make it a subtask.
It made a link in the Note area of the target task instead, which was
not what I wanted.

At that point, I hit "undo." This is when things got strange. It undid
a bunch of things, like moving and renaming the folders.

I hit undo again, the screen flashed, and it reverted back to the
OmniFocus state from my last reboot, and no amount of undo/redo would
bring back my changes and I started getting popup errors about the undo
stack being invalid. Unfortunately, I was too panicked to copy these
for you. The letters "NS" figured prominently in the messages.

This lost a *lot* of work, so I felt obligated to report it. I wish I
could give you a better repro and more detail.

Thanks for working on this soon-to-be-great product.