You can see the join if you know where to look
Which scenes came from the pilot and which were shot in 2001 is largely on the record — and the seam explains several oddities of structure.

01 The pilot footage, the 2001 footage, and what happens at the seam
Lynch shot the original television pilot for ABC in 1999. When StudioCanal agreed to fund a feature completion, he went back to camera in 2001 — not to reshoot anything, but to add. The pilot material runs, very roughly, through the first ninety minutes of the finished film. The 2001 footage is concentrated at the end and in a handful of key insertions. Knowing which is which makes several structural oddities click into place.

02 What the pilot gave the film
The pilot footage is, by television standards, generous — it was shot on 35mm film by cinematographer Peter Deming, which is why the match to the 2001 material is technically seamless. What gives the join away is not image quality but logic. The pilot was designed to open a series: it establishes characters, plants mysteries, and conspicuously declines to resolve them. Betty Elms (Naomi Watts) arriving at Los Angeles Airport, the woman who will call herself Rita (Laura Harring) surviving the crash on Mulholland Drive, the Castigliane brothers' espresso scene, the Cowboy at his corral — these all read as serial hooks, situations that defer their own payoff. Rita's amnesia, in this context, is a television writer's gift: it could sustain a season.
The scenes at Winkie's fall into the same category. The man who describes his nightmare to a companion, walks round the back of the building, and is destroyed by what he finds there — that sequence lands with a force the surrounding plot does not yet earn, because it was never meant to be earned this quickly. It was planted for a later episode. In the feature, the diner scene functions as a structural prophecy about the film's own second half, but that is retrospective meaning, not intended meaning.
03 What 2001 added
The 2001 material is easier to spot once you accept that Lynch was not patching — he was inverting. Club Silencio, the scene inside the blue box, the entire Diane Selwyn storyline, the neighbour with the keys, the final sequence at the Sierra Bonita apartment: these arrive in the film's last section and they do not extend the pilot's world so much as collapse it. Where the pilot poses questions in a register of intrigue and warmth, the 2001 material answers them in a register of guilt and horror.

Angelo Badalamenti's score spans both production periods — he worked with Lynch on both — but listeners who know his catalogue will notice that the later sequences carry a rawer, more exposed texture. The pilot material rides his lush string arrangements; the Diane sequences sit in a more skeletal sound. The music is, in this sense, doing expressive work that the images alone cannot perform.
Rebekah Del Rio's performance at Club Silencio — shot in 2001 — is perhaps the most significant single addition. It is the scene that tells you, without ambiguity, that what you have been watching is a recording. No hay banda: there is no band. The emotion was real but the mechanism was not. That disclosure retrospectively rewrites the pilot footage as dream content, turning a television entertainment into a film about the seduction of entertainment itself.
04 The seam as subject
Lynch has not published a precise shot list dividing the two production periods, and the film is not solved by that information in any case. What the seam gives a viewer is not an answer but a sensation: the moment somewhere around the ninety-minute mark when the film stops being hospitable, when the serial logic that has been carrying you suddenly withdraws its support. The join is designed to be felt. You were watching a pilot. Then you were watching something else.