From what I understand you should be fine. When you register the custom data reference with the AF Server, you are actually storing it within the SQL database. When clients connect, they are able to obtain a copy of the dll. It might be worthwhile to either retire the custom data references, rewrite them or to at least know what is out there. To obtain the registered plugins run ..Program Files\Pipc\AF>regplugin64 /list and Program Files(x86)\PIPC\AF> Regplungin /list.
If they plugins are old, their might only be 32 bit assemblies.
Also from PI System Explorer> Server Properties > Plug-Ins and then look for Data Reference Plugins.
Dan nailed this question-- custom data references are registered and stored in the AF server, and are automatically retrieved by clients and stored in the '%programdata%osisoft\af\plugins' directory. Therefore, when you restore your SQL database, there shouldn't be anything further you need to do in terms of distributing custom data references. In fact, the custom data references are likely still stored on client machines and won't need to be re-fetched until a newer version of the assembly is registered on the AF server.
Hope this helps!