Changes between master file and sub-files using Power Query

[Anonymous]

I have a number of sub-files maintained by others that I have pulled together into a single "master file" using Power Query. However, I have also had a stakeholder make some changes directly to the master file. Will these changes get overwritten when I refresh the master file & it once again pulls in data from the sub-files, or not? Am I right in thinking the best/only way to make changes to the data is to do so in the sub-files? I couldn't find an obvious answer to this online.

[HotChilli]

What is the nature of the changes?  When the data is refreshed, Power Query performs the combine and transform steps for the queries in order.  So are we saying that the stakeholder has edited the steps in PQ?