Pawel,
You should be able to modify an existing transformation rule group via XML and load it in without it creating a new group. Within the GolfStream application as an example, I exported out the HoustonAccounts transformation rule group to XML and saved it to my desktop. I then edited the XML in a text editor and added a new Mask rule to the file and saved it. I then imported the XML back into the application and then went to Account Dimensions > HoustonAccounts Group > Mask and see the new transformation rule that was added to the group. That change then flows to the profiles that the group is included within.
