Most important thing I can think of is, if the db is split and you copy fe and be to another server and delete all data from the be tables BUT you forget to change the linked table paths in your copy, it is quite possible to delete all data from the original be tables. Less chance if on a separate server that has no exposure to the original one, but definitely possible if you copy to a different directory on the same server. When there is no such exposure, the worst you'd likely get is a message saying that the linked table cannot be found when you try to view it.
Might be best to open new db's and import all to it. In the options, import structure only, not data.
The more we hear silence, the more we begin to think about our value in this universe.
Paraphrase of Professor Brian Cox.