I reported this to Apple’s iPhone feedback, but thought I’d post it here in case someone runs into the same issue.
Under specific conditions, adding a new album to Aperture will change the albums that are selected for synchronization in iTunes
To reproduce:
Make sure you have an Aperture library with several projects that contain albums.
In addition, make sure you have some folders that are at the root level and contain albums. (i.e. the folders are not inside a project)
For example:
Project 1
-Project1Album1
-Project1Album2
Project2
-Project2Album1
-Project2Album2
-Project2Album3
Folder1
-Folder1SmartAlbum1
-Folder1SmartAlbum2
-Folder1SmartAlbum3
Folder2
-Folder2SmartAlbum1
Now, go into iTunes and in the iPhone settings, set the iPhone to sync photos from Aperture.
Select the “Selected Albums” radio button.
Select the following Albums to have a checkbox so they will be synchronized to the iPhone:
“In the last month” (A built in Aperture Album)
“Folder1SmartAlbum2″
“Folder2SmartAlbum1″
Now synchronize your iPhone with iTunes.
Now close iTunes
Go to Aperture.
Now create a new album in one of the projects. I.e. “Project1Album3″ and import some photos into it.
Now restart iTunes.
Go to the iPhone photos tab.
You will notice that now that the following albums are selected for syncing:
“In the last month” (A built in Aperture Album)
“Folder1SmartAlbum1″ <- Notice that this is not what you had originally selected
“Folder1SmartAlbum3″ <- Notice that this is not what you had originally selected
You can see that the albums that are set to sync have changed even though you did not change them.
The correct behavior is that the albums you originally selected to synchronize should stay selected.
To me it appears like iTunes is using an index to reference which Albums the user has checked to be synchronized. This if you insert an album prior to an album that has been selected for synchronization the index will now be incorrect. The incorrect index will reference the previous album instead of the correct one. It should be using a name to reference albums, because adding and removing albums is something the user is likely to do. (In my case I add a new album every time I import a set of photos).