if your query is correctly written, then there is no ambiguity and your question is moot...
query should look something like this
Select File1.Field1 as Field1A, File2.Field1 as Field1B,....
both fields have the same name in the original files, but are internally known as Field1A and Field1B
If you use the query editor and look at the created sql code, you will see this in mode details.