I think the safe way to apply patches is to patch the client in the directory that all the others link to first.

For example, I have:

wow1
wow1\Data - real Data directory
wow2
wow2\Data - link to wow1\Data
wow3
wow3\Data - link to wow1\Data

First of all, I update the wow1 copy, which updates the executables and the Data. The updated Data is automatically available to the other installs, but I have to manually copy the executables from wow1 to the other install directories.

This method has worked fine for me a few patches.