OS X "Yosemite" 10.10 and 10.10.1 contain an OS bug which can cause data loss when upgrading Yojimbo stored data from an older (3.x or earlier) version. The primary symptom of this bug is that the relationship between items and tags is lost after upgrading the database, so that tagged items are no longer tagged, and tag collections are empty.
This OS bug has been fixed in OS X 10.10.2. In order to prevent data loss, if you launch Yojimbo under OS X 10.10 or 10.10.1 and a database upgrade is necessary, Yojimbo will present an alert and you will have to update your Mac to OS X 10.10.2 or later before the upgrade can proceed. (In general, we recommend keeping your OS installation up to date, no matter what generation of OS X you use.)
This bug in the OS does not affect Yojimbo installations running on OS X 10.9.5 or earlier.