I have an Investigation file with 4 ontologies recorded. I open this with the Creator, and click "validate". The act of clicking "validate" changes the file on-disk (I know this because I have the file open in a text editor window, which immediately tells me the file has been updated). The update was that Creator has deleted one (or more) of the ontology records. It then complains to me that there is no reference for ontology XXX in the Investigation file (which there was... until it deleted it! :-) )
I have an Investigation file with 4 ontologies recorded. I open this with the Creator, and click "validate". The act of clicking "validate" changes the file on-disk (I know this because I have the file open in a text editor window, which immediately tells me the file has been updated). The update was that Creator has deleted one (or more) of the ontology records. It then complains to me that there is no reference for ontology XXX in the Investigation file (which there was... until it deleted it! :-) )