Learn English – “Owner of” vs. “owner for”

They're both correct and the meaning is essentially the same. I'd say that the preposition choice depends on how you intend to communicate the message.

If you think of the reference as an arrow in a diagram coming from file X to ABC, then from works better as the preposition, as it indicates movement and direction:

ABC should not be referenced from file X.

If you think of the reference to ABC within the boundaries of file X, then it is in that works better as the preposition, as it indicates inclusion within a space:

ABC should not be referenced in file X.

I would probably write the sentence with from in a technical document, as I usually think of arrows and direction when I'm thinking of references between files or objects.

"Principal" has a specific meaning in the context of commercial law. From Wikipedia:

a principal is a person legal or natural–who authorizes an agent to act to create one or more legal relationships with a third party

Effectively, this means that the principal is the business. In the case of a corporation, say General Electric, the principal is General Electric itself, while Jack Welch was one of its agents during the 80s and 90s. In the case of a sole-proprietorship, the business and its owner are effectively one-and-the-same, so a person might realistically be called the principal in that situation, but pretty much no other.