App intermittently disappearing after installation

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We're build a pkg with three apps in it from the command line. There is one primary app and two supporting apps. We build a folder structure inside a temp directory like below (some folder names replaced with generic ones):

mkdir -p ./tmp/Applications/.hiddenfolder/
mkdir -p ./tmp/Library/Application\ Support/Company/
mkdir -p ./tmp/Library/Preferences/
mkdir -p ./tmp/Library/Logs/Company/
mkdir -p ./tmp/Library/LaunchAgents/
mkdir -p ./tmp/Library/Company/
mkdir -p ./tmp/Library/LaunchDaemons/

#Grant Logs Folder Read-Write Access to All
chmod a+rw ./tmp/Library/Logs/Company/
chmod a+rw ./tmp/Library/Application\ Support/Company/

We then build and sign each app dependency and place them into the temporary folder. For each app we're calling:

xcodebuild -workspace "$PROJECT" -scheme "$TARGET" -configuration Release -derivedDataPath "$WORKING" clean build
codesign --force --deep -o runtime --entitlements "../$TARGET/$APPLICATION.entitlements" --sign "$DEVKEY" "$WORKING/Build/Products/Release/$APPLICATION.app"
cp -R "$WORKING/Build/Products/Release/$APPLICATION.app" "$DESTINATION"

The primary app is copied into ./tmp/Applications/.hiddenfolder/ . The other two apps are put in ./tmp/Library/Company/ and ./tmp/Applications/

We then create the component list, build, and notarize the final pkg using the script below:

Some definitions of the variables used below:

IDENTIFIER=com.company.pkg.app1 (not real id but an example)
ROOT=./tmp
SCRIPTS=./scripts
GUI=./pkggui

pkgbuild --analyze --identifier "$IDENTIFIER" --version "$VERSION" --root "$ROOT" --scripts "$SCRIPTS" "$NAME-tmp.plist"

/usr/libexec/PlistBuddy -c "SET 0:BundleIsRelocatable NO" "$NAME-tmp.plist"
/usr/libexec/PlistBuddy -c "SET 1:BundleIsRelocatable NO" "$NAME-tmp.plist"
/usr/libexec/PlistBuddy -c "SET 2:BundleIsRelocatable NO" "$NAME-tmp.plist"

pkgbuild --identifier "$IDENTIFIER" --version "$PKGVERSION" --root "$ROOT" --scripts "$SCRIPTS" --component-plist "$NAME-tmp.plist" "$NAME-tmp.pkg"
productbuild --synthesize --package "$NAME-tmp.pkg" distribution.xml
sed -i "" \
-e '$ i\
\    <title>App1</title>' \
-e '$ i\
\    <background file="background.icns" alignment="bottomleft" scaling="proportional" />' \
-e '$ i\
\    <welcome file="welcome.txt" />' \
-e '$ i\
\    <installation-check script="InstallationCheck()"/> \
    <script> \
        function InstallationCheck(prefix) { \
            if (system.compareVersions(system.version.ProductVersion, '12.0') &lt; 0) { \
                my.result.message = "This update requires OS X version 12.0 or later."; \
                my.result.type = "Fatal"; \
                return false; \
            } \
            return true; \
        } \
    </script>' \
"distribution.xml"

productbuild --distribution distribution.xml --resources "$GUI" --package-path "./$NAME-tmp.pkg" --sign "$DEVKEY" "$NAME.pkg"

Once built and notarized this pkg becomes the base for the installers we give to customers. For each customer we have some custom parameters we set in a plist file inside the pkg, which requires us to expand the pkg out, add the plist file to /Library/Preferences/ in the expanded pkg, and then flattent/re-notarize the edited pkg.

What we're running into is that the primary app (App1 above) will intermittently disappear after installation. We check all of the files we lay down in the postinstall script, and usually it detects the app in the correct location (/Applications/.hiddenfolder/), so it appears that it is correctly laying the files down but something is removing the app after installation. A couple of times the postinstall script has detected that the app is not in the correct place and fails, but usually the install will finish and only the other two apps remain. So far we've found no logs or evidence of it being moved or deleted; it just ceases to exist after installation.

Has anyone else had this issue and found a solution?

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