Export FCP Batch List and import it into the fresh Cinema Tools database. Tell Cinema Tools to connect entries in the database to the media files. Open each clip and using Identify button make sure burned-in KeyKode and CamRoll/LabRoll matches the numbers in the database. Check several times for each clip – a second past the beginning, a second before end and somewhere in the middle in case there are several takes in one file. In case there is more than one camera roll in one file – the KeyKode is not continuous – you must go back to FCP, split the clip and create as many media files, as there are camera rolls. Then import them in FCP, replace all the cuts with these new clips and add them to the Cinema Tools database. When you’re absolutely sure all data in Cinema Tools database is correct proceed to export Cinema Tools film list from the FCP Export Menu.
This all is in the FCP and Cinema Tools manual.