As stated by my colleague Ianko - there is no another possible reason for showing the absolute URL to a file, unless the mentioned filter is enabled. If this filter is not enabled the Editor shows only the virtual path to the files, so the url will be like "/uploads/media/somefile.mp3
The only other option I can think of is that you have a custom logic for editing the URLs, so you can check there (if any).
Unfortunately, we cannot be of much help without being able to reproduce and examine the problematic behavior on our side. Please, isolate the problem into a runnable project or send us a live URL where we can replicate the case, so we can provide you further assistance on this matter.
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