I got an update today for qt5 webengine and I was wondering if I should update it or just remove it since we are on qt6/plasma 6?
Yes. Arch does not support partial upgrades. Always update every package. You can try to delete it, but you might still have a package that depends on it if you have an application that hasn’t yet made the move to Qt6. Also, using Discover for package management on Arch-based distros is not recommended. Discover uses PackageKit for distro packages and its use is discouraged by Arch due to a number of issues.
It’s not even an update, it’s a rebuild to add a missing dependency.