The only thing I can think of is that we have you might have hit the shortcut Cmd/Ctrl - Shift - M to merge all selected items?
The other question is why the crash happened in the first place. You can open the log folder via Help -> Show log folder – should Tropy crash again, the project.log in that folder might help us figure out the cause.
I should say, I am overall very impressed with Tropy. It is filling a huge gap in my research workflow, so thank you all for developing and maintaining it!