Table relationships copied from Datamaker to Subset seem to be stored on a connection profile level and disregard project/version selector. Is there a way to preserve those relationships back to a version or a project in the Datamaker repository?
Release: TDMTDD99000-4.4-Test Data Manager-for Test Data on Demand
At this time, this is working by design, and Subset will only store the relationships to the connection profile itself (which is stored by default in the %appdata%/grid-tools folder).
If you need to preserve these relationships and history, a suggestion would be to version control the connection profiles in a source management system of your choice.