To be able to change product sku with RapidFlow, you need to have the Pro add on.

1. Make a regular product type export with single column in it - sku
2. Export your product's sku, and download the file.
3. Edit the file, remove top row with column name, prefix each sku row with

   %CP

   with no spaces around the code.

4. Add a column after current sku with new sku code, remove the rows you don't want to change.
5. Create import profile of type Products Extra and import the modified file.

cp-sample.csv

##%CP code, old sku, new sku
%CP,sku,new_sku