Never seen that happen. Plugins shouldn't disappear unless you close them. Also not sure bridging works in that direction. Why aren't you using Reaper x64? All my 32-bit plugs work fine that way. I would not think that 64 bit plugins would work on a 32-bit system at all.
It could be that you have the option enabled in prefs/plug-ins to only allow one fx chain window; that would cause it to disappear if you click another track.
If embedding doesn't work in that direction it could be the plugin is still tied to the fx chain window even though it's not actually embedded.
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