How to extract applications as IPA files on iOS9?
If you are jailbroken, there is a solution that can be batch scripted. 

Install sbutils and ipainstaller from cydia 

ssh to phone and run these commands:

sbbundleids &gt; backup.txt
while read line; do
ipainstaller -b $line
done &lt; backup.txt

and then to install the apps:

ipainstaller *.ipa

I tested a few and it allows to upgrade apps directly from app store without fuss. (same appleid, obviously)