Hi,
I think there have been problems with updating audio files before, but this is what happens:
I export a media file from cubase
something needs to be changed within the songs audiofile
I make changes in cubase and export the media file again with the same name (and choose overwrite)
the audiofile within the media file is still the old version, not what I exported.
This is not the way it should work…
this has happened to me before and I realized I was actually opening the old file over and over again, and the new file was actually being saved in a different location. 
Check it.
Unfortunately, this is not the case. I have different folders for the cubase and VSTL projects, and when I export the media file from cubase with the new audio file (the old one is no longer anywhere inside the cubase folder), the vlsprj file is new inside the VSTL folder, but the audio file in the audio folder inside that same VSTL folder is still the old one. So, the vlsprj file is updated, the audio file isn’t. I didn’t check if the same thing happens with data in other folders like tempo, markers and so on…