When a folder is deleted in Automation Engine 12.1.1, its OH_Deleteflag is set to 1 and the OH_Idnr is added to the name, just like when an object is deleted (However, the deleted folder is not displayed in the Recycle Bin). This is new in V12.1.1 and was a necessary change because of the changed search mechanism.
In the Utilities of Automation Engine 12.1.1, there is a bug that causes the DB Unload in batch mode to fail with messages like:
The reorganize database action fails when there are deleted folders.
Release: AUTWAB99000-12.0-Automic Workload Automation-Base Edition
Update to utilities of the fix version listed below (or a newer version if available).
We suggest you always upgrade Automation Engine and Utilities, but in order to resolve this particular issue, it is enough to update the utilities.