Merging Duplicate Guest IDs
There is no 'Merge Duplicate Guest' feature inside of the BookingCenter's Desktop Property Management System. One way you can 'clean up' your Guest database is by exporting the Guest database (directions are found here) and this creates a text file.
Then, use Excel to cleanse the duplicate records into a single row/record.
Then, re-import the 'cleansed' Guest Database into the Desktop system once again (instructions for doing this and the sample format for the required file at: https://support.bookingcenter.com/index.php?/Knowledgebase/Article/View/102/14).
The only problem with this approach is that the bookings that were linked to the 'deleted' guests will now be 'orphaned' and thus, they will no longer be linked to the proper Guest History. There is no way to avoid this result. But from the point of doing this onward, you can be more disciplined in the way you associate bookings to past guests to avoid the problem getting worst.