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I've just tested this on some PRC files and they all work fine. Hmm.. This is the process that the GUI goes through when you open a file initially. When you open a file its converted into a temp MOBI file. Cover image & thumbnail files are extracted to temp files also if they exist. If the opened file is a PRC then the Databasename is extracted and populated into the Booktitle field and the checkbox ticked. The reasons for this is that if you convert a PRC to mobi without specifying the --title flag the longtitle data is populated with the name of the PRC file.
Once you have made any additional changes within the GUI and press convert the changes are made against the temp MOBI file and output to the Output Filename specified.
Nothing happens to a file until you press the convert button. Simply opening a file does nothing except extract metadata information from the PRC / Mobi file. Changes are only commited to the Output File on pressing convert.
Hope that helps....
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