When you are exporting a GEDCOM file from K&KPro with the intention of importing it back into K&KPro, please make sure that you set the "Receiving system" option to Kith and Kin Pro instead of File. This will include all the K&KPro-specific data such as the position of family rectangles. http://kithkinpro.spansoft.org/manual/html/ged_export.php
There is no way of recovering the family rectangle position data if it has not been included in the GEDCOM file.
The other way to transfer your data is simply to copy the contents of the C:\KKPro3Data folder which stores all your databases.