DataImportHandler's FileListEntityProcessor relies on Java's File.list() method to retrieve a list of files from the configured dataimport directory, but list() does not guarantee a sort order (1). This means that if you have two files that update the same record, the results are non-deterministic. Typically, list() does in fact return them lexigraphically sorted, but this is not guaranteed (2).
An example of how you can get into trouble is to imagine the following:
xyz.xml – Created one hour ago. Contains updates to records "Foo" and "Bar".
abc.xml – Created one minute ago. Contains updates to records "Bar" and "Baz".
In this case, the newest file, in abc.xml, would (likely, but not guaranteed) be run first, updating the "Bar" and "Baz" records. Next, the older file, xyz.xml, would update "Foo" and overwrite "Bar" with outdated changes.
"There is no guarantee that the name strings in the resulting array will appear in any specific order; they are not, in particular, guaranteed to appear in alphabetical order."
(2) Even if it was guaranteed, lexigraphical sorting would give you the following sort order: