2 more questions for today ..... Sorry!!

[J-grow]

Ok I added a second deep brood box to a hive about 4 weeks ago or so. 

The hive also had a super on it that 7 of the frames had just been extracted and put back in the super to be cleaned up and refilled and the other 3 frames were full of honey but not capped enough to harvest.

The inspection I did 2 weeks ago I only took the lid off and the super had been cleaned up but hardly any honey in the frames so I didn't go into the new 2nd brood box because I figured that if they were not working in the top super they must be building out comb and doing proper bee things in the new brood box I gave them.

Just now when I inspected the hive the 9 frames spaced honey super is full of honey and each frame is about half capped

Question #1. If I leave full frames of honey that are half capped they WILL keep capping them until there all capped correct?

I then go into the new deep brood box I gave them 2 weeks ago expecting to see hopefully comb built out on the foundation and brood but instead I found 10 full frames of honey all 50% capped and no sign of laying in the second box at all?!

Sooooooo question number 2 is ........... WHAT DO I DO NOW! ...... The entire hive is full and I don't think any of the honey can be removed because it might not be ripe?

As always thanks for your advice these bees are very very humbling

[iddee]

We can't help until we know what is in the bottom deep. If the queen has empty cells to lay in, leave all as is. If not, add a box.

[J-grow]

Your right .........  I guess I need to do full inspections every time!

 I was assuming things and thinking less disturbance is better.

Will they finish capping or do you sometimes have to make judgment calls on when to extract honey?

[iddee]

If it comes in, they will cap. If not, they may or may not move it up and cap.

[Perry]

Bees are very energy conscious, they will usually cap comb when it is ripe. Towards fall however, they tend to sometimes not cap honey even though it may be ripe, especially if they feel they will be using it shortly. You could do a simple shake test of the uncapped honey to see if any comes out, and if not you are probably relatively safe to harvest it, particularly if you use it shortly thereafter.
A refractometer will tell you for sure whether it is honey that is ripe or not.
In the mean time, if that top deep is plugged out I would seriously consider adding another deep between the two, but like Iddee said, first find out what's in that bottom deep.