As good as word studies can be, potentially at least, sometimes an overly thorough word study can over-complicate what is perhaps a relatively simple meaning. This might be one of those times. First, an analogy.
There was a father who sat his son down one day for a heart to heart talk. Unbeknownst to his son, the dad had witnessed recently his son doing and saying some pretty thoughtless and hurtful things in the presence of some young men the dad thought were his son's friends.
Calmly and with great empathy the father shared his thoughts with his son about what he had seen and heard. After suggesting some important principles his son had violated in the way he treated his supposed friends, the dad expressed disappointment in what his son had done and suggested the son apologize to his friends, the sooner the better.
Well, the son was shocked that his dad had witnessed his less-than-stellar behavior, but he refused to accept his dad's words of reproof. What's more, he told his dad he would not be apologizing to his friends--who were no longer his friends anyway. The dad then looked his son in the eyes and said lovingly,
"Son, one day you'll appreciate the wisdom of what I've been saying. Today, evidently, is not that day. One day you'll realize that friends are precious people. They are not to be tossed aside and replaced whenever they get on your case, which is what I suspect they did to you. The Bible tells us in Proverbs, 'Faithful are the wounds of a friend' [27:6]. Sometimes that's what good friends need to do for us. They need to get up into our faces and tell us we messed up. Getting upset with them the way you did was not the smart thing to do."
And now the application of the analogy. Jesus was preparing his inner circle of disciples for his inevitable departure from them. His ascension to the Father would take place just a few short weeks hence, so he wanted to assure them the pieces of the puzzle would begin to fall into place for them at some future time. John used the expression "in that day" (John 14:20; 16:23; and 16:26).
"In that day" (Gk. hmera) and "an hour is coming" (Gk. Hora) are two expressions Jesus uses in John 16, and each expression--though both are time oriented--has a different meaning. I suggest "in that day" is more long term, whereas "an hour is coming" is more short term. More specifically, the "hour" refers to the time immediately following Jesus' crucifixion and burial, but the "day" refers to the days, weeks, and months (even years) following Jesus' resurrection and ascension.
In the brief window of time after Jesus' death on the cross but before his resurrection, disciples such as Cleopas and his companion were certainly confused, sad and dejected. They had pinned their hopes on Jesus of Nazareth, but now that he's dead and gone, their hopes are dashed. Then, unbeknownst to them, Jesus approached them on the Emmaus Road and engaged them in discussion. He also reprimanded them gently for not believing all the prophets had predicted about his suffering first and only then entering his glory(Luke 24:25-26). Slowly, the truth began to dawn on them as Jesus exposited the Tanakh to them, with a particular emphasis on the "things concerning himself in all the Scriptures" (v.27). Finally, as they broke bread together, their spiritual eyes were open, and the puzzle pieces began to fit together.
My point in stressing the two categories of time (viz., day and hour) is to suggest that in the wake of something traumatic (such as the father, above, confronting his son), there comes a brief period of hurt, numbness, and confusion. That is normal. Some people get over that initial phase and enter almost immediately into the freedom and joy of repentance and renewal. For others, however, they require more time to mull things over. That extra time could indicate a hardness of heart or it could simply indicate a slower timetable for processing what happened and then determining what their response should be to what happened.
THE END OF THE NEW STUFF
I suggest Jesus was not saying to his disciples that the minute after he was resurrected or the minute after he was ascended to the Father, they would then realize fully the intimacy of the relationship of the Father to the Son, the Son to the Father, and the Son and Father to all true believers. Now some of Jesus' followers may have "caught on" fairly quickly--perhaps especially some of Jesus' women followers, but some others of them, I suspect (e.g., Jesus' half brother James?), were a little slower to comprehend what had happened once Jesus had departed from them physically.
Put differently, Jesus was assuring his disciples the day was coming when they would know, experientially, that he had not really left them, but that another Comforter, the Spirit of promise, would transform their relationship with him and with the Father into one of intimacy and true spiritual power. And one day, though perhaps on different timetables and in many different ways, the truth would dawn on his disciples and they would then know that Jesus was indeed in the Father, as were they in him and he in them.
In conclusion, my earlier analogy does break down in perhaps one obvious way. The father in my story can only hope the advice he once gave to his son would one day become to his son a transforming truth. Jesus, on the other hand, knew of a certainty that his disciples would eventually put the pieces of the puzzle together, and they would then "turn the world upside down" with the gospel message of a risen Savior.
"At first his disciples did not understand all this. Only after Jesus was glorified did they realize that these things had been written about him and that these things had been done to him" (John 12:16 TNIV).