Your question is not clear. However, the correlative conjunction is 'neither..nor' ('they neither intend...nor have entered'), and we often invert subject and verb in such negations:
Sir: I am really interested in this poster's question. Am I wrong to think that "intend to enter" and "have entered" are not parallel? In fact, should the author express his thought using a NOT ... NOR pattern, such as: The parties acknowledge that they do NOT intend to enter, nor have they ever entered, into a secret agreement. I am eager to have your expert advice on this matter. Thank you.
I see what you mean, Anon– it could be better structured, although the grammar is subtle enough that most native speakers would not acknowledge any problem. However, 'not..nor' is not a very felicitious structure, and I don't see that it is any improvement on 'neither...nor'. I think that I would simply do this: