I am having the same issue but for me it seems limited to parts from the Near Future Technologies mods. All other stock parts and parts from all other mods I have work fine it seems limited to Near Future Electrical, and Near Future Construction. I have however noticed that on rare occasion even in the vanilla game with no mods on every now and then when I go to remove a part from one of the stages the connection node from the stage disappears and I cannot re-attach anything without ctrl-z to simply undo the last change I've done. These are some annoying Issues I have been having with the connection nodes lately both with and without mods installed and I'd like to find out if there may be a fix for this or if anyone else is having the same issues.