If you aren’t using masters from RAWs then this is correct Rob. Just load your old masterdark (from PI) as a dark and create masterdark, then APP wil properly make a masterdark of your old masterdark and it will perfrom analysis on it (check fits header by using details selectbox above image viewer). This also applies to your old masterbias and masterflat.
Load them as a single calibration frame fo the right type and create calibration frames.
One extra tip. Use your masterdark to create a bad pixel Map for your sensor as well ? set the bad pixel map setting at: hot pixels kapp at 2 to start with. This is similar to cosmetic correction in PI I believe.