@enoch I think if you, as a game, wish to have prior RP matter, it's a slippery slope in the context of IC relationships. We all know a draw for a lot of people in these things is playing out various relationships.
Scott/Jean, Logan/Jean, Rogue/Gambit, Emma/Scott, Shatterstar/Rictor, Kitty/Piotr, Kitty/Pete Wisdom, Logan/Scott/Jean/Emma (okay, maybe that last one's going a bit off the rails) - these are all canonical, expected and accepted character relationships depending on the cutoff. But yes, if Scott and Jean are playing one in-game, one of them drops, and a new player comes along and doesn't want to continue it, that's one thing. The new player has every right to go in another direction.
However, I don't think it's fair to the other player to just say "Well, none of that stuff happened now." It essentially invalidates and throws out things that did happen in-game, and it can be a big problem.
If something is logged and posted, it typically counts. If you have a tool in-game (+canon, was it?) that establishes something in a simple one-line explanation, it sounds like it counts as well. If people are doing this and that "off-screen" that becomes more difficult to enforce without proof of it, and we know that happens. In addition, some people don't want to share the mushy stuff with everyone even when it's purely vanilla. I understand if someone wants to keep it private. Using +canon could be a great alternative to posting a log.
But, if it's established and is part of the continuity in any way, my suggestion would be that at least in the general sense, it sticks. If a new player wants to go in a different direction, fine. If the new player and the old player agree to just say "They saw each other for a while and now they aren't" without focusing on any more than that, fair enough.
When someone comes in to play a character that's already been played before, there should come with it an expectation that the former player(s) may have done some things the new one wouldn't have, but it's not an automatic reason to retcon a bunch of stuff immediately. If there are a lot of logs, it's tough to expect someone to account for every little detail so some summarizing may be needed, some info from other players of characters that did things with someone, whether it's a relationship or not. It can make taking on a played character more daunting, but in general it's good for the game if "What Has Gone Before" is maintained as still there somehow.
Most things can be worked around, acknowledged, etc. If there IS a good reason to retcon, figure out a sensible justification and excuse with staff. It's a comic book genre. Strange shit happens. New writers put different spins on characters and change things we've seen in the past. "I was mind-controlled by blah," "Sinister cloned me," "I was stuck in an alternate reality and replaced by a different version of me," "It was a Skrull," or "It was just a phase I was exploring" may be cheesy, but it's not necessarily wrong to go with any of those. Create an RP hook out of it that an existing, affected player can at least do something with, even if it's not perfect. Don't simply toss out the time and effort they put in. Honor it.
Just take it on a case-by-case basis as needed. Be prepared to spend a little time helping hash something out and hope both sides can come away satisfied with the result. Also make sure players who take on a new character that hasn't been played before understand that anything they do that's available for all to see can normally be expected to stand.