How to resign a Swift ipa and preserve SwiftSupport directory structure

For the majority of our applications, we either have the source code or access to the .xcarchive file, and are able to either export the ipa from Xcode, or run the 'xcodebuild -exportArchive' to generate the signed ipa. Unfortunately, we receive one application from a vendor who is only able to provide us with an ipa file.

In the past, these builds were entirely obj-c and in order to resign, we simply replaced the embedded profile, updated the bundle id, and then ran codesign on the .app file. Where the codesign command would update entitlements, certificate, etc. to match our account's identity. Once the codesign command completed, the modified .app file was copied into a 'Payload' folder and compressed into an ipa file.

Unfortunately, the vendor just upgraded their application to Swift and the ipa they provide us now has the 'Frameworks' folder in the .app file, as well as a 'SwiftSupport' folder in the top level folder of the ipa (next to Payload). I am able to run our usual steps just fine, but have also added a step to run the codesign command on the individual libraries in the 'Frameworks' folder of the .app file. This works fine and the frameworks are resigned with our identity. However, the output of the script is an ipa with just a 'Payload' directory, no 'SwiftSupport' directory.

As expected, this fails when uploading through Application Loader to iTunes Connect, as it expects to have a 'SwiftSupport' folder. Unfortunately, if I manually copy the resigned 'Payload' and the original 'SwiftSupport' library into a zip folder and rename it to ipa, the error message from Apple still says, "Invalid Swift Support - The SwiftSupport folder is missing. Rebuild your app using the current public (GM) version of Xcode and resubmit it."

Unfortunately, since we only get the ipa from the vendor and don't have the source code ourselves, we aren't able to rebuild the app with Xcode and export the resigned ipa.

So my question is whether there is a recommended way for resigning a Swift ipa if one doesn't have the source code or initial .xcarchive? How is that SwiftSupport folder generated and added to the bundle? (outside of having to export from Xcode and select 'Save for iOS App Store Deployment')

Thanks!