I have noticed that the options I specify for Manual Refinement (particularly under the "Reconstruction" and "Masking' subsections) are not what appears after the job is done and I check the "Show Job Details" in the Results section (see attached). Which set of settings were actually used under the hood?
As an aside, I notice that the value of the "Reconstruction ID" looks like some integer overflow is happening somewhere? It no longer changes between rounds of refinement, and I certainly haven't initiated quite that many jobs.
I'm hoping my database isn't corrupted! I had to do quite a bit of manual editing of the picks to get things right, which I would prefer not to have to redo. If so, is there a fix less drastic than backing up the appropriate tables of interest from the sqlite database and starting from scratch?