TL;DR - "Merged" is too strong a word. The characters may be present, but most of the events from Vertigo and Wildstorm titles are ignored in the DCU books.
Flashpoint didn't really merge the Vertigo universe into the DC Universe - more like it just returned "ownership" of two characters (Swamp Thing and John Constantine) and their supporting casts (in this case, mostly meaning Abby Arcane and Chas, John's cabbie friend) to the DCU.
There's little to no reference to the bulk of their Vertigo time. John still has a tree tattoo, I believe, so Tefe Holland (Alec and Abby's daughter, with John as sperm donor/surrogate) may be in continuity, but she hasn't actually been referred to to date. And, I believe that storyline happened before the creation of the Vertigo line.
Both John and Swamp Thing were seen in the DCU again immediately prior to Flashpoint, so it's somewhat arguable that the "merger" even happened in Flashpoint; however, it was post-Flashpoint that each of the two had there own DCU series again.
As far as other Vertigo characters with a foot in the DCU:
The Vertigo version of Shade the Changing Man appeared in the Secret Seven Flashpoint book, and in the first story arc in Justice League Dark (2011). After that, he disappeared again.
Animal Man and the Doom Patrol had both returned to the DCU years earlier.
Sandman Mystery Theatre was always basically set in the DCU, although it mostly avoided contact with the more, ah, colorful DCU characters from that timeframe. Still, there was some crossover into DCU titles - I believe there was a storyline in Starman that included Wes Dodds as he was seen in the Vertigo title.
Although they've been intimately tied to the DCU in the earliest days (via Dr. Destiny and the WWII era Sandman), the books tied to Sandman are still in Vertigo territory for the most part. With Death's guest-shot in one of the Superman titles shortly before Flashpoint being the only reason I added "for the most part".
Side note: the "Young Animal" sub-line seems to be part of the DCU, with a lean in the direction of Vertigo. Really, not dramatically different from the pre-Vertigo books that moved into Vertigo. That includes both the recent Doom Patrol run, and the Shade the Changing Girl/Woman titles.
Wildstorm is simpler - basically, I believe any Wildstorm property that someone's interested in is now available in the DCU. We've seen several members of WILDC.A.T.s, Stormwatch, and the Authority (off the top of my head: Voodoo, Grifter, Fuji, Jack Hawksmoor, Jenny Quantum, the Engineer, Midnighter, and Apollo). The New 52 actually had a Stormwatch comic for over two years, with some ties to the Demon Knights title (the name being tied in, as the WILDC.A.T.s fought the Daemonites, an alien race). We've also seen Caitlin Fairchild (from GEN 13) in Ravagers. We had a Team 7 comic, featuring both DC and Wildstorm characters.
That said, again, it doesn't seem like the old Wildstorm titles have necessarily been merged into DCU continuity. The basic characters and some of the relationships between them seem to be intact, but the original sotrylines from those comics are not referenced. And, by the time of Rebirth, the only Wildstorm characters that seem to still be active are Midnighter and Apollo.
Not to mention that, starting in 2017, we have The Wild Storm (with one spin-off so far), Warren Ellis' reinvention of the Wildstorm universe, with no connection to the DCU. Not sure if this moved the Wildstorm characters (editorially speaking, at least) back out of the DCU or not. I can't think of any Wildstorm characters in DCU titles at present (i.e., in 2018).