Project w/ 2 app targets loses linked libraries to 2nd app after Xcode modification

I have a moderately complex XcodeGen set up involving multiple internal libraries/frameworks and produces multiple application targets. It works great, until you try to modify the project in Xcode (e.g. by adding a new file). Xcode then ends up stripping the libraries from all but the first application target(!)

Simplified Reproduction

I've created a simplified example project to illustrate the issue:
XcodeGenBugExample.zip

1. Download the .zip, use make to run xcodegen on the 3 included projects

➜  XcodeGenBugExample
 make
⚙️  Generating plists...
⚙️  Generating project...
⚙️  Writing project...
Created project at /Users/mthole/XcodeGenTest/LibraryA/LibraryA.xcodeproj
⚙️  Generating plists...
⚙️  Generating project...
⚙️  Writing project...
Created project at /Users/mthole/XcodeGenTest/LibraryB/LibraryB.xcodeproj
⚙️  Generating plists...
⚙️  Generating project...
⚙️  Writing project...
Created project at /Users/mthole/XcodeGenTest/App/App.xcodeproj

2. Open the App.xcodeproj, and examine the App1 and App2 targets. They both link to the libLibraryA.a and libLibraryB.a libraries. All is well.

3. Go and add a new .swift file to the App target. (Or do a number of other Xcode operations that trigger whatever re-evaluation is happening...). I added File.swift to the App1 and App2 targets.

4. Examine the App1 and App2 targets. Notice that App2 is now missing both libLibraryA.a and libLibraryB.a. Sadface!

We expect App1 and App2 to still be linked to both libraries. Mysteriously, only App1 is!?

Next Steps

I've been using Xcode 12.4. If anyone has any ideas, I'm happy to help investigate further here.

Use the attached XcodeGenBugExample.zip and run make to generate the three projects, then inspect App.xcodeproj with its App1 and App2 targets. Reproduce the issue by adding a Swift file to both targets in Xcode; done means both targets still link libLibraryA.a and libLibraryB.a after the modification.