I am not sure what to do with the expressions you supplied. Is this something I can pass into a --filter, or this for the UI still?
Yes, all of the files have the (1)..(4), but some 'episodes' are longer or shorter(some have 7 parts, some have 3). Will that matter?

Is there a way to do this via cli? This is a remote machine and I don't have the UI to use.

So I have all of my Doctor Who files, which have a naming convention like this: Doctor Who - S01E01 (001) - An Unearthly Child - Parts 1-4: -Doctor Who - S01E01 (001) - An Unearthly Child (1) - An Unearthly Child.avi -Doctor Who - S01E01 (001) - An Unearthly Child (2) - The Cave of Skulls.avi ...