Personally I wouldn't use either one.  I use the kiss principle.  So in saying that, I would probably say "add" that to the file or "put that in that file" or "update that file".  I usually use append at the document level, i.e. "append that document".  Interfile isn't really used, in my opinion.  I use the acronym "PA" (put away).  I agree with Julie that they probably both could be used to say the same thing and as Julie says, it could create "blurriness".  This is where a Core Subject Thesaurus or Controlled Subject Vocabulary is important in an organization.  This will provide employees with standardized terminology for use in the indexing and retrieval of information. A controlled vocabulary ensures that a subject will be described using the same preferred term each time it is indexed, making it easier to find all information about a specific topic.

Append

attach something: to attach or fasten something to something else and/or
to add extra information to something, especially to a document

Interfile

file with others: to put an item or items among similar items in a file

John A. Gervais
Program Manager
Policy and Guidelines Section
Information Policy and Governance Division
Statistics and Information Management Directorate 
Corporate Strategies and Business Development Branch 
Canada Revenue Agency
320 Queen St., Place de Ville, Tower A, 6th Fl., 
Ottawa, ON, Canada, K1A 0L5 
Tel: 1-613-946-0245
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