To reproduce my scenario: take Amplitube 3, the x86 vst plugin, edit some stuff randomly in a program, export the program and bank while in x86 Cantabile, then open it in x64 Cantabile or x86 Cantabile: works fine. Now, export a program and bank while in x64 Cantabile, and open it in either x64 Cantabile or x86 Cantabile: nothing happens, the plugin state and the bank won’t change.
The danger is that you can export to overwrite a bank you use and update frequently accidentally in x64 mode, and you lose all your presets.
This has to do with jBridge, obviously, but that is about as far as I can figure out.