I believe these versions replace the originals. Comparing before and after inventories, I still have the same VST3 files, just with higher version numbers (1.0.2.3 -> 1.0.3.84).
However, after the update I also have two
new files, which appear to be the VST2 versions, with .DLL extensions rather than .VST3.
Note that VST2 and VST3 siblings will have different IDs, and will therefore not be considered equivalent by SONAR. I believe they can even be mixed and matched within the same project.
I am not experiencing any problems with either of them.