If something in your processing system requires you to be changing the files that you are taking in, in order to "preserve" them. Then you might want to ask whether you are using the right system or process.
It might often be advantageous to create a derivative of an original with a different file name, but that should probably be considered a derrivative rather than an original (it might be considered a new preservation master though).
On the other hand, if you document the renaming process and it is easily reversible then it might be worthwhile. Especially if it enables you to take other actions to preserve the content that you might not otherwise be able to take without having renamed the files (e.g. ingest them into a problematic but ultimately more effective preservation system).