Hello,
Backup Logbook Pro prior to your sync (File..Archive..Backup). When syncing to Logbook Pro for the first time set the DATE setting on the bottom of the PDA Wizard to the date of your first APDL flight being sync'd in. From there it will sync new flights and you shouldn't lose older data. Logbook Pro by default looks for "newer flights" but backing up Logbook Pro and manually setting a date for the first sync will be added protection.