Taking a step back, what are those .acrodata files actually used for? If they just store trusted certificate information that, if needed and the file isn't present, is automatically downloaded again from a trusted source (e.g. Adobe.com) then it would seem to not be a particular problem to just rename/move the old files, and I can let users know that they might experience a brief delay when they open a document the first time.
However if those files store something unique per user then finding a way to import them will be necessary. In our environment, telling a lot of people how to manually handle a popup will not be seen as a great approach.