Sorry, I should have been more clear about that. I didn't mean "issues" in the sense that it would break, but that it wouldn't be as straight forward as having the files being alpha ordered according to where they were found in the file. For instance, 123ab would be ordered before 123d but would have occured 24 times after 123d.
So if you wanted things files to be alpha ordered by the order of occurance, and you were going to have a significant amount of duplicates (or rather a chance of haiving more than 26 duplicates), then you'd probably want to start with 'aa' as your base.
Thanks for pointing that out CountZero.