Renaming a clip in the Project Panel will not break the link to the media file.
You can also use the 'Comment', 'Description', 'Log Note' and 'Scene' columns
to input scene organization information instead of altering the file name (which can
sometimes make tracing the original media file on disk more difficult).
You should use a sequence setting that matches
the majority of the footage you intend to use.
SD footage will of course be problematic in a 4K timeline.
I'm afraid there probably isn't a good way to scale SD to 4K...
unless it originated on film and you can go back to transfer.
Magic Bullet Instant HD works pretty well upscaling SD to HD.
when you say renamiong can "sometimes make tracing the original media file on disk more difficult"
I am referring to file management on disk as it relates to the Project.
For example if you load all of your media and change the file names,
then discover that there is something quirky with a particular file... it will
make it more difficult to trace on disk for evaluation.
It will not affect the media reference in .xml export at all.