Anyone worked out how to update the VST3 of the latest Rapture Pro update (update 3) as on my system the VST 2 and AAX files are updated but the VST3 version remains on V2.00.2.541. have checked the install directory and the file hasn't been modified suggesting the file is not in the install package.

All I recall doing is installing via CCC, in verbose mode, I think it gives you the options of what to install, can't really recall, just go through the motions, and I have version 2.00.3.96 VST3 installed.

Tried the install without CCC and it worked this time

If you haven't already, in the options CCC you can set it to verbose mode for installations, I believe this is basically the same as doing manual install with the same options but with the benefits associated with installing via CCC like it being able to keep track for updates etc.
 
Anyway glad you got it sorted.