As Freud's personal doctor, Max Schur, revealed, in 1899, when Freud was finishing The Interpretation of Dreams, he could gloss over his wish to survive Fliess which necessitated "killing him off" in fantasy. (1) Maybe not only in fantasy.
Recounting their last meeting, in August 1900, in Achensee, Austria, Fliess wrote, Freud showed a violence toward me. Subsequently, Fliess confided a... sinister version … 
it was Freud’s intention to lure him into a lonely mountainous region, then to push him over a precipice or into water below. Fliess claimed he escaped because he had cause to suspect Freud’s intention.(2)
A case in point: Fliess was a man of very small stature and he could not swim.(3) We know about Freud's attempt on Fliess life because he shared this story with his daughter, a niece, and a lifelong friend,
In The Psychopathology of Everyday Life published the year after their fateful meeting, Freud himself revealed that he was struck ... by my companion’s rejecting my proposal for a longish expedition and objecting during our short walk to taking a certain path which he said was too steep and dangerous. (4)
Luckily for Fliess, he erred on the side of caution.  In the past, the two, now former, friends, used to meet regularly for their dates, aka congresses, in which, besides looking for victims - killing can be fun - they exchanged views, ideas, and sexual fluids, This was their last "congress".
(1) Schur, Max, Freud: Living and Dying, (1972, p. 171).
(2) Malcolm., Janet, In the Freud Archives, (1984, pp. 132-133).
(3) Malcolm, (2002, p. 122-123).
(4) SE 6, p. 211.

How could Fliess have known about the danger? Writing to Fliess on October 3, 1897, Freud confessed that,
My nephew and younger brother determined not only the neurotic side of all my friendships, but also their depth.  There's no doubt, Fliess knew that both of those relatives were deceased by Freud's hand. Notably, Schur, pointed out that,
This was an amazing confession to make to Fliess, implying … that Freud's friendship with the latter contained neurotic elements (1), thus a murderous intent. Fliess got the hint. There were others.

Freud's fake dream

Two years later, a year before their fateful meeting in Achensee, in his letter of September 21, 1899, published in, Freud alluded to his murderous animosity towards Fliess stating,
In the non vixit [he did not live] dream I find I am delighted to have survived you. And he adds pointedly, is it not hard to have to hint at such things - to make them obvious, that is, to everyone who understands? (2)
Fliess certainly understood. Notably, the fake dream deals with revenants, thus, the two of Freud's deceased former "friends”, Fleischl and Paneth.
In the alleged dream, Fleischl, Fliess, Paneth, and Freud, sit at a table.
This is what happened in Freud's dream:
My friend Fl. [Fliess] had come to Vienna ... in July. (July is the month named after Caesar, thus relating to Caesar's death.)
Fl. tells about his sister and says: "In three-quarters of an hour she was dead," and then something like: "That is the threshold." ... Fl. ...asks me how much I have told of his affairs. Whereupon, seized by strange emotions … I say:  Non vixit. [he did not live].