Talk to the Player
You can talk to the player about it, and discuss the usage of the dagger. Explain to them that it's throwing off the game, and needs to be removed. If they agree, then problem solved, and you can discuss the best way forward.
If they don't agree with you, then unfortunately, for the sake of the game, and the rest of the group, you'll likely have to put your foot down. In this instance however, removing it entirely will likely seem too harsh, so compromising by simply nerfing it (maybe giving it a limited amount of charges, or a 1 in 10 chance to paralyse, etc.).
Develop a scenario for it.
This is kind of dependant on whether or not you talk to the Player about it first. If you do talk to the Player, and they decide they don't want to get rid of it, you'll have to handle it a bit differently.
But, in the case where the player agrees with you, and you do decide to remove it, perhaps a scenario where the original owner of the dagger wants it back. A powerful being has come for it (the PCs can try and keep it for themselves, you know... RP it out a little), but ultimately, the owner takes it back, and vanishes, or perhaps at twist ending, the owner is killed by the party, but with it, the power of the dagger also dies.
The options for how the dagger is removed are endless, and can be built to match your campaign (stolen, dropped down a ravine, etc.).
Alternatively, as user Darq was kind enough to provide, replacing the item may be a better solution. As in their comment, this can also be RP'd into the game, making it a more enjoyable experience
"You bury the dagger into the heart of the immortal beast, and while you cannot truly kill it, the paralytic power of the dagger holds it fast, trapping it until a future fool pulls the blade from its chest. Conveniently, this also lets you pry the sword from its hands."
Ultimately though, it sounds like the PC isn't going to just accept losing such a powerful weapon, especially when they complain about enemies with resistances. The underlining thing about D&D is that it's meant to be fun for everyone, including the DM, and the rest of the players, and having such a powerful item in the game is ruining that fun.