Sorry for the confusion and inconvenience here! OS X includes the concept of "File Packages", which are folders with a special attribute that tells the Finder to hide the contents and present it as if it were a file. If you control-click a file like this, you'll see a "Show Package Contents" entry in the context menu; that reveals the otherwise hidden contents.
In your case, one of the files in the package appears to be missing - the file that contains the "root" transaction that your subsequent changes flow out of.
It's hard to tell what exactly caused the situation you're seeing - it's possible that it's a bug in OmniFocus, sometimes backup software is at fault, or it may just be a disk error while writing out the data. If you zip up the database and send it to our
support ninjas we can take a look and try to determine what happened.
In the meantime, OmniFocus makes frequent backups of your data to protect against situations exactly like this; if you select
File -> Revert to Database Backup...
and choose your most recent backup, you should be back up and running.
If you do notice anything important is missing since your last backup, let the support ninjas know that and we can assist.