I recently upgraded from an iPhone 4S to an SE and successfully transferred everything.
Today I took a photo using the new phone and wanted to download to my Win7x64 system. Previously all I had to do was plug in the phone and it would appear in my devices and as a removable drive in Windows Explorer. The iPhone SE did not appear in Windows Explorer, and in Devices and Printers it showed up as "Apple USB Driver" instead of "iPhone". At this point it was appearing just fine in iTunes.
I deleted the device driver and let the system reinstall it, which restored desktop access to the photos on phone. It appears in Windows Explorer, but curiously no longer as a removable device.
However, since that point, every time I plug it in I get the "Allow this device to access photos and videos" prompt on the phone, but the phone does NOT appear any more in iTunes. I suspect somehow Windows is treating it like a permanent device instead of removable and is preventing iTunes from seeing it.
So far I've rebooted both the phone and the computer (several times each) and reinstalled iTunes.
Not sure what to do next.