Solution:
Unzip the IPA
unzip Application.ipa
Remove old CodeSignature
rm -r "Payload/Application.app/_CodeSignature" "Payload/Application.app/CodeResources" 2> /dev/null | true
Replace embedded mobile provisioning profile
cp "MyEnterprise.mobileprovision" "Payload/Application.app/embedded.mobileprovision"
Re-sign
/usr/bin/codesign -f -s "iPhone Distribution: Certificate Name" --resource-rules "Payload/Application.app/ResourceRules.plist" "Payload/Application.app"
Re-package
zip -qr "Application.resigned.ipa" Payload