This issue can be solved by copying the plugin folders or .dll’s from the original location in to the new N5.5 folder. 
In N5.5 my UAD-2 'Powered Plugins are no longer available from the ‘Insert’ dropdown menu and the program reports that it can not find the various UAD plugins used in the current project.
It also no longer recognizes the BFD2 drum sample plugin!
Everything works as it should if I load the same project using N5.1.1
Worryingly, the following appears in the Issues and Solutions pdf on the Steinberg download site:
Projects created in Cubase 5.0 / 5.2 64 bit using “JBridge” for 32 bit plugins may not load - Solution: Please consider to use VST-Bridge instead.
Does this mean we have to re-install all plugins currently running via Jbridge? - If so, can Steinberg guarantee that VSTbridge will now be able to do everything that Jbridge currently does?