I'm sorry, I did post a bit too quick, and did the double check I made wrong (original post remains striked through below).
The source of the problem is quite different:
When importing an application xml, this xml can be malformed so that it produces an error on import and additionally seems to break the database, resulting in the application (and probably some/all others, didn't test that) not showing up any more and re-emitting the error on every start of ketarin.
In this special case, I manually edited the xml, duplicating a variable entry, renaming the "key" but missing to rename the "name" node, so the name was there two times. I think ketarin should discard anything tried to import when an error occurs on import to avoid the database being corrupted by this.
When I export one of my applications to a file, delete it, and re-import it afterwards, I get an error "Failed to import file: Ein Element mit dem gleichen Schlüssel wurde bereits hinzugefügt" (german for "an element with the same key has already been added"). The same error message appears when exiting Ketarin afterwards, and starting it again. I did not look into the db file, but I suspect the application does not really get deleted in the first place but only marked as deleted, so the key (name) duplicates when reimporting.
