So I was thinking about Arthur's sons lately, as I wanted to modify my upcoming campaign to include Gwydre as a fourth bastard, with the three main points being:

-He was conceived when Arthur was still a squire unaware of his heritage, being born just before the fateful First Tournament (his mother is an Irishwoman named Aillean Grey-Hem);
-Because of this, he becomes Arthur's personal favorite, reminding him of simpler times, and as such comes close to being recognized as heir, however;
-He dies during the hunt for the Troit Boar

Thinking about this, however, has made me have to deal with something that's always rubbed me the wrong way - Borre and Loholt co-exisiting. It's generally well-accepted that Malory's Borre is the same person as Wolfram's Loholt, and this shows in the GPC: They have similar names, their mothers have nearly the same names (in fact, the GPC calls Sanam's daughter/Borre's mother Lyzianor when she shows up, only to call her Lyanors in Borre's biography and give the name Lyzianor to Loholt's mother!), and they're born in the same year. I'm wondering how to deal with this, since it's grown into a bugbear upon my back. I've narrowed down a few options:

-Ignore it. The easy answer, admittedly, but I find it unsatisfying.
-Remove Borre. Arthur has three sons; Gwydre (son of Aillean), Loholt (son of Lyzianor of Bedegraine), and Mordred. All three suffer the fates they have in the GPC or, in Gwydre's case, the Mabinogion. This has the added advantage of removing Borre's rather lackluster death. The disadvantage is it removes a character from Malory
-Remove Loholt. Arthur has three sons; Gwydre (son of Aillean), Borre (son of Lyzianor of Bedegraine), and Mordred. All three suffer the fates they have in the GPC or, in Gwydre's case, the Mabinogion. This has the advantage of removing a dark episode of Kay's story, but, again, Borre's fate leaves much to be desired.
-Change Loholt's name to Llacheu (his Welsh counterpart).This has the advantage of removing my main grievances, but people associate Loholt with Logrin and Kay more and Llacheu is going to be murder to pronounce for non-Welsh

I was wondering what other people think and if they've ever experienced similar problems

I ignored all of them, except Mordred, but even his paternity was in question (by the players, in-game no one ever suggested that he was anything else except Lot's son). Part of my reason was that the players had never heard about any of them (save Mordred) before, and I had more than enough on my plate rather than introduce a couple of Arthur's bastards into the story only to have them die off. I especially disliked Kay being such a knave in the Loholt story. Instead, our Sir Kay was a dick, sure, but he was still a worthy Knight of the Round Table, and died during the Grail Quest.

I do agree with you about the Borre-Loholt overlap. I'd keep Borre, to be honest, if I had to choose. Both of them die around the same time anyway, but Borre is much more fun to have around (proud and boisterous), and it keeps Sir Kay from being a villain. If you are bothered by Borre's death and would like it to be something different, change it! (All the more so since I can't find his fate in Malory on a quick search... All I can find is him coming to court under the name of Borre, and being present at Urre's healing under the name of Bohort. Almost a portmanteau of Borre and Loholt! :) )

There is of course a fifth option: You could integrate the stories of both Loholt and Borre. Take the parts of both stories that suit you best.

I do agree with Morien that the stories are not well known and do not seem to impact the larger story much, although it will reveal reasons why Arthur keeps Mordred close as it is his last living child, even if it is revealed that Mordred is working against his best friend.

Okay, so I've decided to go with the following:

Gwydre is the eldest, and the only one who was with his father from the beginning. As such, he has the personality (and stats) that the GPC gives Borre - courteous but condescending, a good man but acting like he's going to become king, especially as Guenever's barreness becomes more apparent. Between Norgales being his homeland and being in Arthur's court in the early years, he finds himself drawn to the Gales clan and even serves as Lamorak's squire. He also becomes known as a skilled hunter. In 548 his kinsman Culhwch enlists his aid (along with Kay, Bedivere, Gawain, presumably the player knights, Arthur's hound Cabal, and a handful of other RTKs - by 548 I'm assuming that the bulk of the players are RTKs or glorious enough that they're being considered) in hunting the Troit Boar (As depicted in the GPC). Although they succeed, the boar kills Gwydre. Kay loses it (blaming himself for the death of Arthur's son) and winds up roaming the wilderness until he becomes a village priest (as a nod to Lancelot's fate in "Excalibur"). The Troit Boar adventure, then, takes the place of the Gilded Box event.

Borre is more similar to GPC Loholt here. Coming into Arthur's life relatively later, Borre finds himself drawn to the Ganis knights. A knight who preferred adventure to court, he finds himself thrust into the limelight after Gwydre's death, a position he finds uncomfortable. In any event, he doesn't last much longer. Unlike his GPC death (which was simply a pastiche of the death of Richard the Lionheart) Borre lives to join the Grail Quest - however, he, along with other knights like Griflet and Dodinel, is kidnapped and imprisoned in the Dolorous Prison by Brian of the Isles. Although Lancelot frees them, Borre catches an illness in prison and dies on the way back to Camelot. His appearance at the Healing of Sir Urre is Malory getting confused by Sir Bors and Sir Ozanna also being there.

Thus, Sir Mordred doesn't declare himself until 557 at the Lancelot Tournament - him being named heir literally starts the Twilight Period. Unsurprisingly, Mordred works with (well, uses) the Orkney faction.