I recently had my NEX4000 professionally installed and finally got around to adding the U260 Navigation add-on. 

The Nav works great, is ultra responsive and has a lot of customization opportunities.

The issue? Its one or the other between having the GPS or my iPhone connected. The iPhone is connected using HDMI/Lightning Cable to the Apple Adapter. It works flawlessly. The GPS is connected using the yellow connector on the left back side of the unit. When I turn the car on, the Navigation button is highlighted and works great. As soon as I connect my phone however, the navigation button disappears and only the Apps button remains. Pressing the mode button or menu button do not bring up the Navigation and the button is nowhere to be found.

Any help you can provide is greatly appreciated!

I recently had my NEX4000 professionally installed and finally got around to adding the U260 Navigation add-on.

 

The Nav works great, is ultra responsive and has a lot of customization opportunities.

 

The issue? Its one or the other between having the GPS or my iPhone connected. The iPhone is connected using HDMI/Lightning Cable to the Apple Adapter. It works flawlessly. The GPS is connected using the yellow connector on the left back side of the unit. When I turn the car on, the Navigation button is highlighted and works great. As soon as I connect my phone however, the navigation button disappears and only the Apps button remains. Pressing the mode button or menu button do not bring up the Navigation and the button is nowhere to be found.

 

Any help you can provide is greatly appreciated!

Sadly there isn't yet a solution for you.

Your nav unit connects via the same method as the 30 pin iPhones. As such the pioneer head unit sees this as a video input just like the HDMI you are using for your newer iPhone. The 4000 doesn't do both inputs at once so just like how Bluetooth and usb stop working the second you plug in your HDMI, so does your nav. It's a very odd av input system on the NEX line.

The NEX4000 is marketed as having both on Pioneer's website. 

I'm a little pissed if this is the case:

http://www.pioneerelectronics.com/PUSA/Car/DVD-Receivers/AVH-4000NEX

It describes both the iPhone and GPS connectivity and even shows photos of the Apps button with the Nav button on the same screen (with NEX4000 labelling, NOT NEX7/8000)

From the Pioneer NEX4000 Page:

If the above is true, then how is Apple CarPlay meant to work if the Navigation add-on is installed?

I have the same issue, hopefully the firmware update will solve this problem. As for now, it is either nav or appradio. Kinda sucks, because unlike the screen pictured on web, nav and appradio app is in same place, and when av adapter is connected, nav dissppears. I just don't use appradio. And plug iphone directly on usb1. I too am ticked off, after spending 300+ on U260. If carplay cancels our nav, i will start blowing up pioneers phone line with calls.

Just got off the phone with Pioneer after a 40 minute wait.

The hardware is not capable of supporting both functions. It will always be one or the other. Pioneer should have had that documented somewhere, their site is incredibly misleading - it shows both apps and navigation buttons on the 4000 page. It highlights AppRadio and Navigation. The Pioneer rep looked everywhere for where it would say that its not able to do both and couldn't find anything...

"THAT WOULD HAVE BEEN NICE TO KNOW YESTERDAY."

Thankfully Amazon has a great return policy. I'm sending both the 4000 and U260 back and will be ordering the 8000. 

if you dont mind me asking but what is the point of buying the radio and a separate piece for the nav function? at that point wouldnt it make more sense to buy a unit with both already intergrated together

Didn't want to spend $1k upfront.

Wanted to try out the GPS apps included with AppRadio which are good not great, see if I could get AppRadio Extenstions to work/see if the dev released the iOS7 update.

gotcha

if you dont mind me asking but what is the point of buying the radio and a separate piece for the nav function? at that point wouldnt it make more sense to buy a unit with both already intergrated together

In my case, i ordered last years model, and paid for it. then got an email stating out of stock and they were sending 4000nex in place. i really had not done any research on the nex line. i just wanted dvd player for the 2 and 4 year olds. After receiving the head unit and installing with all the add ons to keep steering wheel controls, chime and bypass, i started researching and learning all about it. Thats when i figured on adding the u260. i liked the idea of built in nav. Especially with the buggy app radio. Only after the install, did i find out about app radio canceling out nav. Either way, i love the nex and love the u260. I just wish everything worked like the website shows. 

If I am understanding correctly this is only a problem when using appradio? Or is it also a problem when connecting an iphone via lightning cable / usb ?  I never use appradio as it feels cobbled together imo but was just curious about this problem.

Only when using appradio

Only when using appradio

If this is the case it may be possible for the U250 and Carplay to play nice. No guarrantees, but there is a chance in 2016 when Pioneer launches carplay for this to work. 

Here is what i do now and what i will do with iphone 6. Since the only real app i use in appradio is dashcommand, i hook up iphone to usb1(therefore i have functionality of all that intails), then i run dashcommand on phone(in mount horizontal) and this way i have functionality of everything i use. iphone 6 will have bigger screen, and i may get iphone6+, dont know till tomorrow and what is available. I found dashcommand works fine with ios 8, as a stand alone app.