You can run a csv export with Store Commander to extract product prices as well as margins.
You can then adpat the prices accoridng to the margins, and apply the modification by importing that same file.
Your export mapping will include the following fields:
Once prices have been changed in the csv file, you can import it to apply the modification.
The import mapping will include id_product (which is your identifier) and the prices you want to modify: price excl. tax OR price incl. tax + vat, wholesprice.
The margin can be imported because it's a calculated value.