Edit: As of Xcode 9.1 Beta you can upload In-App Purchase content from Xcode’s Organizer window. This is far more convenient than using the Transporter tool as described below.
As of v3.7 Application Loader no longer supports In-App Purchases. Instead, you have to use Apple's command line Transporter tool to upload content.
You can install Transporter separately to XCode / Application Loader. I prefer to do this as I find it cleaner and can update it in isolation. You can find the instructions here:
https://help.apple.com/itc/transporteruserguide/#/apdAbeb95d60
An example workflow for updating an existing in-app purchase's content would be thus:
Step 1 : Get the existing metadata for the in app purchase:
iTMSTransporter -m lookupMetadata -u "$ITC_USERNAME" -p "$ITC_PASSWORD" -destination "$DOWNLOAD_PATH" -vendor_id "$ITC_PRODUCT_PARENT_ID" -subitemids "$ITC_PRODUCT_ID" -subitemtype InAppPurchase
You can omit the -subitemids and -subitemtype options if you wish to simply download the metadata for the entire app and all of its IAPs.
I believe you can also edit the other metadata relating to your app itself. You may also be able to remove/omit certain sections and still get the process to work.
Step 2 : Update your local copy of the metadata
Drag the new IAP content, which you should have archived into a .pkg file using XCode, into the .itmsp directory the previous step generated.
Update the size and md5 checksum in the region of the xml file which carries that information. The md5 checksum for your .pkg is obtainable by opening terminal and typing "md5" then dragging and dropping the .pkg into terminal and pressing enter.
Step 3 : Verify the .itmsp package
iTMSTransporter -m verify -u "$ITC_USERNAME" -p "$ITC_PASSWORD" -f "$ITMSP_PATH"
Step 4 : Upload (assuming verification was successful)
iTMSTransporter -m upload -u "$ITC_USERNAME" -p "$ITC_PASSWORD" -f "$ITMSP_PATH"
This workflow was taken/adapted from the following website, which is extremely helpful and carries other relevant information you may want:
http://www.cyrilchandelier.com/having-fun-with-itmstransporter