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Yes, this is all possible! You can input and output to one or multiple files within a workflow (including xlsx). If you wanted to automate this process you would need Alteryx Server to schedule it - in Designer you'd have to manually kick off this process yourself.
Yes, if it's unknown which rows might have changed, then I'd just compare my rows in the file at the start of the workflow with those at the end (using a join); anything that comes out the Left/Right would be a row that has had a change in it - just this flow of data could then be sent to output.
Hope that makes sense - happy to send over an example if you prefer?