For some reason when I perform owner maintenance in SherWare and then synchronize with QuickBooks I end up with a new Customer in QuickBooks, but the same owner (modified, of course) in SherWare.

If the Owner Name is modified in SherWare, and then the owner file is synchronized with QuickBooks, it will add a new Customer: Job to QuickBooks for that new Owner Name. The Customer: Job that is added to QuickBooks is based on the Owner Name field within SherWare. If you had only made changes to any other field in the Owner Information screen other than the Owner Name field, it would not have added a new Customer: Job to QuickBooks.

I would recommend that you merge the old Customer: Job with the new one that was added using the most recent Owner Name.
To merge the old Customer: Job with the new one, change the name of the previous Customer: Job in QuickBooks to be exactly the same as the new Customer: Job that was added after modifying the owner name in SherWare. When you do this in QuickBooks, it will tell you that there's already a Customer: Job with that name, do you want to merge them? Answer yes, and they will merge including their history in QuickBooks.

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