Yes...but you'll need to know something about them...either name or VariantID, or something about them that makes them different from the others. My guess is, that if the other 5000 products existed before the import AND you haven't added any after then you could update only those 10000 products with
Code:
update dbo.ProductVariant set FreeShipping=1 where VariantID > #
where # is the VariantID of the last ProductVariant record that you don't want updated. If you've got them all mixed and matched (eg. the first 3000 products are not free shipping, then the next 5892 products are free shipping, then 2 aren't, then 17 are, etc...) then you'll have to make a list of each of the variants that are not free shipping (there are less of them so it will be easier) and then run sql to update only the other ones
Code:
update dbo.ProductVariant set FreeShipping=1 where VariantID not in (#,#,#,#,#,#,#,#,#,#)
where #,#,#,#,#,#,#,#,#,# is a comma separated list of the VariantIDs of the products that do not have free shipping.