It’s really easy to do from the command line. I had a gist of a script for doing this. It has now been incorporated into the ipa_sign script in https://github.com/RichardBronosky/ota-tools which I use daily. If you have any questions about using these tools, don’t hesitate to ask.
The heart of it is this:
CODESIGN_ALLOCATE=`xcrun --find codesign_allocate`; export CODESIGN_ALLOCATE
IPA="/path/to/file.ipa"
PROVISION="/path/to/file.mobileprovision"
CERTIFICATE="Name of certificate: To sign with" # must be in keychain
# unzip the ipa
unzip -q "$IPA"
# remove the signature
rm -rf Payload/*.app/_CodeSignature
# replace the provision
cp "$PROVISION" Payload/*.app/embedded.mobileprovision
# sign with the new certificate (--resource-rules has been deprecated OS X Yosemite (10.10), it can safely be removed)
/usr/bin/codesign -f -s "$CERTIFICATE" Payload/*.app
# zip it back up
zip -qr resigned.ipa Payload
Your new signed app is called resigned.ipa