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For a while I had a similar issue where I would get an excel file every week that I had to append to old data. What I found was that the extract made subtle changes to dates and formatting that caused my data append to yield funky results. I added the data sources separately and looked at the underlying data to see this. I realized that I could make changes to each new excel file to make sure everything was exactly the same, or I could just append the data manually myself within the excel file and create a new connection then replace the old connection.
I settled for the manual way. It's a bit more work but I don't run into any surprises when analyzing my data because I know exactly what I'm putting in. I'm sure plenty of people use appending without issue but with this one funky export, it was more trouble than it was worth for me.