Best Practice for this would be the following.
IN CRM Create a field called Master Record(Field type=Check Box) (Say for contacts) tick mark one contact for which multiple entries exist.
In the Autosynch, add the following filter
"Master Record" = 1 or true(Depeding upon the field type value set for this field in CRM)
This will only fetch the contacts having a "Master Record" equals 1 or true. Thus you would not have duplicates and only modify the contacts in CRM having value of "Master Record" equal to 1 or true.
Do the same while sending the data to CRM