Data import/update on Custom Objects

Hi,
We are using the Custom Object1 for capturing site data within an opportunity. Since the custom object does not have capability to check for duplicates, the users have now entered data into this object which have lot of duplicates and also the data quality and integrity is lost. I am trying to see if there is an option to export this data and reimport them back after cleansing the data.
I then realised while importing custom objects, the only available option is to use external id.All the site that have been entered by the users do not have any external unique id. Also there is no option to do a mass delete records within the custom object1.
I understand that the only option to cleanse and reimport them back into ondemand is using web services. I want to use web services as last option.
Is there any other option to reimport them back into ondemand using the import utility after cleansing the data.
I would like to know what is the best practice while using custom objects. Is it advisable to populate a default value in the external unique id for custom objects while creating new records. If i had populated some value in the external unique ids while creating those records, i would have had the option to update the existing records. Now i don't even that option.
I am looking for some suggestions for this issue.
Thanks
Swami

Bobb,
I exported the data and mapped the row id to the external unique id. Like i said before, the external id is blank in crm ondemand when it is created. We did not have any default value specified for the external unique id.
When i tried to import with overwrite option, it does not find a match.
I get the following error message as i expected.
Row Id: AEMA-EYGFE     No matching record has been found. The import process will ignore this record.
Row Id: AEMA-F8CPC     No matching record has been found. The import process will ignore this record.
Row Id: AEMA-12CLIA     No matching record has been found. The import process will ignore this record.
Unless i do a web service update of External Unique ID in crm ondemand, the import option will not work.
Thanks
Swami

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