OK I used the Mail app to test the troubleshooter and here is what it came back with:
Starting Diagnostics...
File: 'Mail.app'
Path: '/Applications'
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Check file cache database...
✅ File cache integrity is ok
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Check if file is readable...
✅ Alfred has permissions to read this file.
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Check file is in search scope...
✅ File exists within Alfred's default search scope
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Check if volume '/' is indexed by macOS...
⚠️ Indexing may not be enabled on this drive
/:
Error: unexpected indexing state. kMDConfigSearchLevelTransitioning
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Check direct file metadata...
⚠️ Direct metadata is missing, this file is likely not indexed by macOS
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Check mdls file metadata...
❌ macOS metadata missing essential items
/Applications/Mail.app: could not find /Applications/Mail.app.
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❌ Troubleshooting failed