Hope this is useful to you, I found this in the Help Index of Legacy:
Compare Two Files for Duplicates
This feature compares the individuals in the current family file with the individuals in another family file. This way you can see if there are some possible duplicates in another file. No combining of information is done…possible duplicates are only displayed for you to see. As you find duplicates, you can tag them to make it easier to import the parts of the file you might want to combine with your family file.
To use this feature, click Compare Two Files for Duplicates on the Tools menu.
This, of course, would be useful after you have downloaded your file from Ancestry and then compared it to the other Legacy file that you already have. I love the idea about using the tags to flag changes. I will have to try that myself.