Placing Waystones on a ship made with the Valkyrien Warfare Mod causes the Waystone to disappear ("to hide"), while the fully working waystone is still there.

Due to the way waystones are implemented currently, even if there wasn't any visual issues you wouldn't get the expected behaviour, as the position of a waystone is expected to never change. This is planned to be improved in the Minecraft 1.13/1.14 port (#161), but no idea if it's going to help with the valkyrien warfare handling.

Waystones still do not support being moved after placement in 1.14, but it's no longer completely out of the question.

Waystones should support being moved by other mods now