Hello,
I also had a lot of problems uploading a file using the Baserow b"Make an API call" block. But with Make - or N8N - you can also use a regular HTTP request. Check the screenshot below for the values you need to enter. In my scenario, the file came from Telegram, but all file sources are possible.
Concerning the duplicate row, I think you need to combine a check if a certain ID exists with removing the row if a value is returned. Both methods can be found in the API documentation of your base. Just check the required parameters and insert them in your Make block