He (sorta) remembered her, at least according to the film's official screenplay.
The bell tinkles again.
JACOB looks up and is thunderstruck all over again: it’s QUEENIE. They
stare at each other – QUEENIE beams, radiant. JACOB, quizzical and
totally enchanted, touches his neck – a flicker of memory. He smiles
Fantastic Beasts and Where to Find Them: The Original Screenplay
And the actor seems pretty convinced that his memory was returned when he saw her.
Alison: It’s the best. So that actually brings us, though… If they’re having a complex relationship, does Jacob remember what happened [in the] last film? It’s kind of hinted at at the end, but it was never confirmed, so…
Dan: I think he does have… yeah. It’s not explained exactly why, but he does have some recollection for sure, yeah.
Alison: Okay. So there’s not a period where he has to relearn everything.
Dan: Relearn everything! And he’s reading this scroll before…
[Alison and Cat laugh]
Dan: “Ahh, okay, I’m back [unintelligible].” No, I think you see at the end of the first one. It comes flooding back to him
EXCLUSIVE: Dan Fogler Talks Queenie and Jacob and More in “Crimes of Grindelwald” at Comic-Con!
We also now have an update relating to Fantastic Beasts 2: The Crimes of Grindlewald. Evidently his memories of the Wizarding world were confirmed by Queenie's presence. Before that they were dreamlike.
Felicia Grady: What parts from the first film did Queenie have to catch Jacob up on? Did Jacob remember the Erumpent incident?
Alison: That’s a good question.
Felicia: Because he forgot all the bad memories.
Dan: Yeah, I think he remembered a lot of it.
Alison: Weren’t there Erumpent puffs?
Dan: Erumpent puffs, Niffler muffins… It’s like Midsummer Night’s Dream. Have you ever seen Midsummer Night’s Dream, where Bottom wakes
up and he’s like, “I think I had a dream,” but he’s not sure? That’s
what I think happens to him. You guys all saw it. The poison, the
Thunderbird shower, the Obliviation spell… It erases bad memories and
he didn’t have any bad memories.
Felicia: Even the Erumpent was a good memory?
Dan: Even the Erumpent was a good memory, yes.
Alison: She was good. She liked you so much.
Dan: Exactly. He may not remember the scary parts of it, but he definitely remembers being in the case. And looking over it and he
just being like, “Hey?” It became familiar. So he retains it. Puts it
in his heart. It seeps into his art form with the muffins and
everything. And he had his Titania, his dream girl, and then she walks
into the bakery. I think he’s got the scar in his neck. I think that’s
the one thing where it’s like, “Where the hell did I get that crazy
scar in my neck?” Then it all comes flooding back when she’s smiling
at him. Or a lot of it.
Alison Sudol and Dan Fogler “Crimes of Grindelwald” Roundtable Interview
This is confirmed in the dialogue for Fantastic Beasts 2
NEWT: But you were supposed to have been Obliviated!
JACOB: I know!
NEWT: So . . . But . . .
JACOB: It didn’t work, pal. I mean, you said it, the potion only erases bad memories. I didn’t have any. I mean, don’t get me wrong, I had some weird ones. But this angel . . . this angel over here, she filled me in on all the bad parts, and here we are, I guess, huh?
Fantastic Beasts 2: Original Screenplay