You are not recommending overwriting the new control files are you? That could very well break the hotfix provided by the update.
I posted this earlier, but here it is again. My two pence, anyway! :)
There are 8 files that get modified by the install and you DO NOT TO JUST OVERWRITE THEM. Doing so may void the security patch. The files that are updated can be found on the CD in the path ev60_sp3_284461\Enterprise Vault 6.0 SP3\Enterprise Vault 6.0 SP3\Server\OWA2000s\6.5.*.*.*\Controls folder. Currently the latest we look for is OWA_HF 6.5.7651.25
If your version is above this you should contact support and not just go overwriting them or modify the files directly. For example, the file EV_ctrl_Tree.js in 6.5.7226.0 has our modification going in the file at line 502, however, the same file in 6.5.7651.25 goes in at line 1510. So from base 2k3 to 2k3sp2 there have been over a 1000 lines of code added. If you overwrite just that file you might pooch you OWA install all together.
While it may seem like a quick fix, it is definitly not a good idea, IMHO!
You can. however, do some research of the files and compare where the modifications were going and put them in that same location, but you can't just blindly use the line numbers in the files, as that location is bound to change from sp and patches. AND ALWAYS MAKE COPIES FIRST!!!