The Vampire Killer was first used to destroy Dracula in 1476, by Trevor Belmont. After this, it was passed down through the generations of the Belmont family until the 18th century, when it came into the possession of Richter Belmont. After Dracula's defeat by his son, Alucard, in 1797, the Vampire Killer disappeared and the duty of opposing Dracula was taken up by organisations such as Ecclesia. Although the whip's exact location went unknown for some time, it eventually fell into the hands of the Schneider family, and later into the hands of the Morris Clan, who had been entrusted with holding the whip and using it until the rightful time, 1999, when it would be needed by the Belmonts once more.
The Vampire Killer ultimately returned to the Belmonts by 1999, when Julius Belmont sealed it in Dracula's Castle to weaken Dracula during the Demon Castle War. Julius retrieves the whip during the events of 2035 and uses it against Soma Cruz. Julius again uses the whip during the events of 2036.
It always made me wonder how the whip got from Richter to its later users. This is my theory...
**POSSIBLE SPOILERS**
First, let's look at what we DO know. After SotN's true ending, the whip obviously stays with Richter for quite some time, but we're told that the Belmonts disappeared in the 1800s and were replaced in their duties by organizations like Ecclesia. Nathan Graves used a whip in CotM (1830), but I think we all agree that it was not the Vampire Killer. The next time it appears after Richter is in the hands of Reinhardt Schneider (1852), but then it's absent during the events of Bram Stoker's Dracula. Or at least, we know that Quincey Morris does not use it in the showdown against the count, instead stabbing him with a Bowie knife. Despite this, Quincey's son John gets the whip somehow, even though he was only two years old when his father died and couldn't have actually followed him around the Transylvanian countryside as Bloodlines (1917) implies. John dies from the Vampire Killer's effect on non-pure Belmont descendants, and his son Jonathan inherits it for Portrait of Ruin. With Julius, the pure Belmont bloodline suddenly reappears, he seals Dracula in the Battle of 1999 and leaves the whip inside the castle, only to retrieve it 36 years later.
Now, let's consider the plot holes and how they may be filled logically.
Richter was angry with himself over being mind-controlled, and it wouldn't be much of a stretch to think that he never had children or even an apprentice. Or if he did have children with Annette, he may not have wanted his child to share his vampire-hunting fate, even though we know that the whip eventually came back into the Belmonts' possession. Upon Richter's eventual death, the Vampire Killer must have been passed to another relative, possibly separated from the Belmonts by marriage or other family connections. We can assume that it fell into the care of a Schneider ancestor, who I believe must have originally lived in Wygol village during Ecclesia.
Now, according to the events of Ecclesia, we're told that Wygol village was home to the last known descendants of the Belmont clan (which would have included the Schneider and Morris families). If we believe that Ecclesia's loose 1800s timeframe was actually closer to the mid-1840s (somewhere between Circle of the Moon and Legacy of Darkness, since the Belmonts were also absent during those events), what if Professor Van Helsing of Bram Stoker's Dracula was actually a prodigious student of Ecclesia prior to Barlowe's fall? If that were true, and it is totally believable considering Van Helsing's knowledge of Dracula and the arcane, then he could have been privy to the Belmont connection to Wygol village. He may have even made the acquaintance of some of the villagers during and after Ecclesia's main story.
Reinhardt may have been the son of one of Wygol's residents, which would logically fit his age, and he must have taken up the whip unaware of its true power. In that case, Dracula was acting through Malus and was attempting to force reincarnation instead of waiting for his 100-year resurrection. He would not have been at full power, but he probably believed that he could get away with it since no Belmonts were around. As a result, Reinhardt was able to defeat him without pushing the Vampire Killer's power to its limit, plus he had the assistance of Carrie Fernandez. He may have escaped the Vampire Killer's deadly effects because of this, but he probably suffered some adverse reaction anyway, perhaps enough that he would have sought to get the Vampire Killer out of the Schneiders' possession.
If Reinhardt was suffering ill effects from the Vampire Killer and realized that it needed to be in the care of a higher authority, he may have asked Van Helsing for help. The young professor would have helped treat Reinhardt and would have undoubtedly been excited to take the Vampire Killer off his hands until a proper Belmont wielder could be found.
Of course, people of Belmont blood are drawn to Dracula and his castle like moths to the flame, and although the Morris family had apparently emigrated to America following the events of Ecclesia, Quincey found his way back to London and eventually Transylvania for the showdown depicted in the Dracula novel. My guess is that the Morris and Schneider families decided to separate from their common residence in Wygol to prevent Dracula's forces from being able to corner them in a single location ever again, with the Schneiders staying in Europe while the Morrises left for the American West.
I like to imagine that Van Helsing had a secret conversation with Quincey in 1897, identifying him as a Belmont descendent and entrusting him with the Vampire Killer. Van Hellsing probably believed that reuniting the whip with a Belmont would greatly improve their chances of slaying the Count, but Quincey would never have actually wielded it because he was never trained to control its power. Instead, I assume Quincey kept the Vampire Killer concealed under his coat, and although the whip's presence may have weakened the Count enough for Van Helsing's / Jonathan Harker's party to succeed, it may have also been the reason why Quincey couldn't survive his injuries. Van Helsing would have logically taken the whip back from Quincey post-mortem, since the rest of the party would have been completely unaware of its role in the battle.
Now, let's assume that in their secret talks, Van Helsing also questioned Quincey about his young son and why he was courting Lucy in the first place. Van Helsing was often intrusively straightforward anyway, and he would be interested in the future of Quincey's bloodline. Quincey would have revealed that he was actually back in Europe to find a suitable home for his two-year-old son John, whose mother died in childbirth. Quincey states that he cannot raise a child by himself in the wild American West, and it is his hope to gain the favor of a wealthy English family to adopt John. After Quincey dies in the fight against Dracula, Van Helsing takes up his cause and finds a home for John Morris. He selected the Lecarde family of Spain for several reasons: 1) They possessed another powerful artifact/weapon called the Alucard Spear that had a rich history of demon-slaying as recognized by Van Helsing's Ecclesian mentors, 2) They had a son close to John's age, and 3) Their home in Spain would keep them out of Dracula's sight until John and/or Eric became strong enough to face him.
Van Helsing would have left the Vampire Killer in the Lecarde's care, along with Quincey's Bowie knife and other belongings for John. We know from Castlevania lore that the Vampire Killer carries memories of its past encounters with the Count, and if the whip was around John and Eric as they were growing up, it may have given them false memories of following John's father in the fight against Dracula. By the time they were of age (1917), John and Eric would have been fully prepared to bring the fight to Elizabeth Bartley, the daughter of a long-slain vampire lord who exalted herself by claiming Dracula as her "uncle". Of course, John's usage of the whip eventually killed him, and it passed to his son Jonathan for the events we're all familiar with in Portrait of Ruin.
After Jonathan and Charlotte manage to save the lives of the Lecarde twins, I imagine that the two families helped one another locate a suitable Belmont heir for the whip, since the twins obviously have the most intimate understanding of the Vampire Killer's powers yet seen in the Castlevania series. Julius may have been the first to claim the surname Belmont once again, as he was obviously of pure blood even if his family's name had been obscured by marriage or immigration. This may have been intentional, of course, as the Belmonts may have cast aside their surnames in their time of weakness, in order to protect themselves and their children from Dracula's vengeance.
In 1997, 100 years after the events of Bram Stoker's Dracula, the Count could have been resurrected, but learning from his past defeats (and possibly sensing the reappearance of the Belmonts), he willingly delayed his awakening, knowing that the solar eclipse of 1999 would bring him to his absolute pinnacle of dark power. Nevertheless, Julius was ready for him, and with a band of compatriots that likely included members of the Belnades, Danasty, Morris, and Lecarde families, he killed Dracula and sealed his power once and for all. To accomplish this, he decided to strengthen the seal by leaving the Vampire Killer inside the Demon Castle itself, but because of the whip's memory effects, separating from it also caused Julius to develop amnesia. This is resolved when Julius meets Soma Cruz and retrieves the whip in Aria of Sorrow. The rest is history.
That's my theory on all of those so-called plot holes, and I would love to hear your thoughts on it.