You should have added the new formats to the book records when you did the conversion using
calibredb add_format. That would avoid the book matching problem and guarantee that the new epub is added to the correct book record.
Are you saying that the new epubs are already stored in the calibre library directory structure? I don't know what would happen if you did an add_format of a file that already exists in the correct directory. The add_format command could easily fail by trying to copy the file onto itself. You could try it with one to see what happens.
EDIT: or you could move the format out of the calibre file structure then use calibredb to move it back.
Personally I would clean the library then redo the conversions, adding the formats one by one as they are created using add_format. If the new epubs are in the calibre library structure then you can easily remove them using Library maintenance / Check library.
EDIT 2: Or just do it en mass in the GUI, avoiding all the scripts.