Without context, this question can only be answered in the most general ways, but even though I'm not a tech writer or tech editor, I've researched the issue a bit. I hope this will be helpful. Any tech writers or editors here, please feel free to comment or correct any errors -- or both.
You're referring to two concepts: Abbreviations ("Engine" for "Core Distribution Engine") and initialisms ("C.D.E." or "CDE" for "Core Distribution Engine"). Either one allows for a kind of shorthand to a long term in continual use. Either can introduce problems or obfuscate, particularly when there are many such abbreviations or initialisms/acronyms.
(The intialism is sometimes erroneously referred to as an acronym, but an acronym is usually just an initialism that spells out a speakable word, or can be tortured to become one. e.g., Nick Fury runs the Supreme Headquarters International Espionage Law-enforcement Division - SHIELD. Also see The Yahoo! Style Guide, and - my personal favorite entry on acronyms - The Jack Lynch Guide to Grammar and Style.)
Your question asks about referring to an often-used concept in a paper in a shortened, convenient way. If the acronym/shortened term/initialism is used consistently and clearly, and defined on first use, you could abbreviate "Core Distribution Engine" as "CDE". But first, ask yourself if you really need to do this. Unless using the full term often would make the writing seem unbearably stilted, or you have an internal style sheet or convention indicating otherwise, ask if you have the option to use the full term more often. Perhaps some of our tech writers can weigh in on this?
What the major style guides say
Are you using any particular style manual? APA, Chicago, MLA? Do you have any departmental conventions or style sheets to follow?
Here's what APA has to say about abbreviations:
To maximize clarity, APA prefers that authors use abbreviations sparingly. Although abbreviations are sometimes useful for long, technical terms in scientific writing, communication is usually garbled rather than clarified if, for example, an abbreviation is unfamiliar to the reader.
Some abbreviations may not be in the dictionary but appear frequently in the journal for which you are writing. Although probably well understood by many readers, these abbreviations should still be explained when first used.
...and from the OWL website for APA style:
When abbreviating a term, use the full term the first time you use it, followed immediately by the abbreviation in parentheses.
According to the American Psychological Association (APA), abbreviations are best used only when they allow for clear communication with the audience.
AP's "Abbreviations and Acronyms" entry, while not as applicable to technical writing as is APA, is worth noting:
... in general, avoid alphabet soup. Do not use abbreviations or acronyms that the reader would not quickly recognize.
The Chicago Manual of Style (10th edition, 10.3 "Abbreviations") takes roughly twice as much text to say essentially the same thing, but they do stress that abbreviations are more appropriate in a scientific and technical context.
The term "Engine" on its own could easily be mistaken for the word engine, but it'll depend on the sentence. I suppose "The user should use the Engine to perform the task" could be confusing in certain contexts (which engine? The CDE, or any old engine).
Whatever you choose to do, be consistent (i.e., CDE or C.D.E. - pick one and stick with it) but clarity is more important than consistency. Haven't referred to the CDE in a while? Perhaps it should be defined again. Do you have a style guide or departmental style sheet? Apply that, but don't let it override your judgment.
Finally, this question is difficult to answer without more text from this paper. Is it possible for you to give us more context?