You can achieve the desired SKU swaparoo using the following steps:
Export Current Products:
Login to Magento Admin UIX -> Navigation: System > Export > Products -> Choose "Entity Type" = Products -> Choose "Export File Format" = CSV -> Click on Continue
Perform Product Transformations:
1) Make 3 copies of the file that was downloaded. Let's call them:
* Products_Original_Backup.csv - This is something that will help us roll-back in case of a SNAFU scenario.

* Products_Original_ToBeEndDated.csv - This is the file you will use to end-date existing products.

* Product_Updates.csv - This is the file you will make Product edits to

2 a) Open the Product_Updates.csv
file - in a text editor - and make necessary edits to the requisite product attributes.
A few tips while performing this task:
- Please make sure you specify the NEW SKUs in the appropriate fields corresponding to configurable/bundle/grouped products. The following files should give you a better idea on the attributes of importance - and the requisite content/formatting - for these product types:
$MAGENTO_HOME/dev/tests/integration/testsuite/Magento/ConfigurableImportExport/Model/Import/_files/import_configurable.csv
$MAGENTO_HOME/dev/tests/integration/testsuite/Magento/BundleImportExport/Model/Import/_files/import_bundle.csv
$MAGENTO_HOME/dev/tests/integration/testsuite/Magento/GroupedImportExport/Model/Import/_files/grouped_product.csv
Friendly Tip: I would recommend against using Excel, as in my experience, it tends to mess up the content/encoding of the CSV file.
2 b) Open the Products_Original_ToBeEndDated.csv
file - in a text editor - and remove all columns except the SKU field. Add another header field called status and assign the value as 0
3 a) Import The Product_Updates.csv
file.
System > Import > Choose "Entity Type" = Products -> Choose "Import Behavior" = Add/Update -> Choose "Stop on Error" -> Click on "Select File to Import" and navigate to the location of the Product_Updates.csv
file and select it -> Click on "Check Data" -> If there are no errors, Click on the "Import" button.
3 b) Import the Products_Original_ToBeEndDated.csv
file.
System > Import > Choose "Entity Type" = Products -> Choose "Import Behavior" = Add/Update -> Choose "Stop on Error" -> Click on "Select File to Import" and navigate to the location of the Products_Original_ToBeEndDated.csv
file and select it -> Click on "Check Data" -> If there are no errors, Click on the "Import" button.
Trust, But Verify!
At this point, you'll need to verify two things (primarily):
(a) The OLD SKUs should've been disabled.
(b) The NEW SKUs should be active.
Some of the important Places/Flows to check:
- Product Catalogs
- Product Details Page
- Order 2 Cash flow
- Searches
- Checkout
- Historical Orders
- Returns Flows
Before File Import

AFTER Product Update CSV File Import

AFTER Disable Old Products CSV Import

Note: In case something goes awry - you can always rollback by reimporting the Products_Original_Backup.csv
file.
P.P.S: You will also need to end-date/disable/delete the new SKUs. You can do this via the CSV approach outline in 2b or directly from the Admin UIX.