Hi,
You said that “File A has a table with external source (another file on OneDrive)”, how do you get the file content from another file on OneDrive? Are you using a flow to get the file contents?
No, I am using external data connections in Excel to do that. Maybe let's start over.
Really there are 3 files:
source.xlsx - simply one row and a few columns of data
destination.xlsx - has a table with data from source.xlsx (excel connection)
flow.xlsx - file with a Table that Flow writes into
Table in destination.xlsx has 1 row. Any time I open destination.xlsx, Excel refreshes its connection to source.xlsx and pulls fresh data from there. Once I save it, Flow kicks in and transfers that row of data from destination.xlsx to flow.xlsx. I get one new row in flow.xlsx each time flow runs.
So in simple words Flow only takes one row from destination.xlsx and adds it to the table in flow.xlsx.
Problem is, once Flow touches (via Get Rows) destination.xlsx the connection between source.xlsx and destination.xlsx is broken.
I have to go in Excel and re-establish it.
Here's how to set up the connection in Excel I'm taking about.
(Filenames on screenshots are a little different)
1. In the destination.xlsx, go to New Query -> From other sources -> From Web
2. Paste source.xlsx URL

3. Then you sign in

4. Load it in, and there you go - Excel just created a table with connection to external source.

5. Go to connections (on Data tab on the ribbon) to see if the connection works.
6. Now, save the file and run FLOW on this table in destination.xlsx. Use Get Rows and write the row to another file.
7. After it's done, go back to check the connections in destination.xlsx. It will not work.

What is even more crazy is that if I have several tables in destination.xlsx with several sources, all those connections will be broken (even if Flow only touches one!).
So in a nutshell, FLOW modifies Excel files in a way that breaks their external data connections.