Unfortunately choosing option 1 (clear all product data then import data) will delete existing records so there's a big chance that the imported product/versions records will get different IDs. Its still possible to get the same IDs with this option though if you just edit and add new data at the end of the same spreadsheet you used when you did your first data tool import.
Also, importing from spreadsheet/csv files shouldn't affect existing order/invoicerows records as they're saved separately. The invoicerows table stores the V_Codenumber, V_Name, V_Price and V_tax values for the orders. For the saved baskets, the items are linked via V_ID field so they are the only the ones that will be affected. Can you let me know how many records do you have in tblKartrisSavedBaskets? If its only a handful I think it should be possible to run a query to replace the old item IDs with the new ones. The saved basket items records are actually stored in 'tblKartrisBasketValues' table so it should be possible to list them out using this query ->
SELECT DISTINCT tblKartrisBasketValues.BV_VersionID, tblKartrisVersions.V_CodeNumber FROM
tblKartrisBasketValues LEFT OUTER JOIN tblKartrisVersions ON tblKartrisBasketValues.BV_VersionID =
tblKartrisVersions.V_ID WHERE (tblKartrisBasketValues.BV_ParentType = 's')
After the import you can then issue another query to update the records one by one->
UPDATE[tblKartrisBasketValues] SET [BV_VersionID] = PUTOLDIDHERE WHERE [BV_VersionID] = PUTNEWIDHERE