So I ran sfc /scannow and all of the apps returned.
there was quite a bit of repairing - 34 components.
\Microsoft\Windows\Start Menu\Programs\Accessories\\Steps Recorder.lnk from store
2022-03-07 13:05:53, Info CSI 0000027a [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\Component Services.lnk from store
2022-03-07 13:05:53, Info CSI 0000027b [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\ODBC Data Sources (64-bit).lnk from store
2022-03-07 13:05:54, Info CSI 0000027c [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Accessories\\Paint.lnk from store
2022-03-07 13:05:54, Info CSI 0000027d [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\Print Management.lnk from store
2022-03-07 13:05:54, Info CSI 0000027e [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Accessories\\Quick Assist.lnk from store
2022-03-07 13:05:54, Info CSI 0000027f [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\services.lnk from store
2022-03-07 13:05:54, Info CSI 00000280 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Accessibility\\Speech Recognition.lnk from store
2022-03-07 13:05:54, Info CSI 00000281 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\Task Scheduler.lnk from store
2022-03-07 13:05:54, Info CSI 00000282 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\Disk Cleanup.lnk from store
2022-03-07 13:05:54, Info CSI 00000283 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Windows PowerShell\\Windows PowerShell ISE.lnk from store
2022-03-07 13:05:54, Info CSI 00000284 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Windows PowerShell\\Windows PowerShell ISE (x86).lnk from store
2022-03-07 13:05:54, Info CSI 00000285 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\Registry Editor.lnk from store
2022-03-07 13:05:54, Info CSI 00000286 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Accessories\\Windows Fax and Scan.lnk from store
2022-03-07 13:05:54, Info CSI 00000287 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Accessories\\Windows Media Player.lnk from store
2022-03-07 13:05:54, Info CSI 00000288 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Accessories\\Notepad.lnk from store
2022-03-07 13:05:54, Info CSI 00000289 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\Security Configuration Management.lnk from store
2022-03-07 13:05:54, Info CSI 0000028a [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\Event Viewer.lnk from store
2022-03-07 13:05:54, Info CSI 0000028b [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\System Tools\\Task Manager.lnk from store
2022-03-07 13:05:54, Info CSI 0000028c [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\Computer Management.lnk from store
2022-03-07 13:05:54, Info CSI 0000028d [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\Memory Diagnostics Tool.lnk from store
2022-03-07 13:05:54, Info CSI 0000028e [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\RecoveryDrive.lnk from store
2022-03-07 13:05:54, Info CSI 0000028f [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Accessories\\Remote Desktop Connection.lnk from store
2022-03-07 13:05:54, Info CSI 00000290 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Accessories\\Wordpad.lnk from store
2022-03-07 13:05:54, Info CSI 00000291 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Accessories\System Tools\\Character Map.lnk from store
2022-03-07 13:05:54, Info CSI 00000292 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\\Immersive Control Panel.lnk from store
2022-03-07 13:05:54, Info CSI 00000293 CSIPERF - FilePI Queue 165ms
2022-03-07 13:05:54, Info CSI 00000294 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\System Information.lnk from store
2022-03-07 13:05:54, Info CSI 00000295 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Accessories\\Math Input Panel.lnk from store
2022-03-07 13:05:54, Info CSI 00000296 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\iSCSI Initiator.lnk from store
2022-03-07 13:05:54, Info CSI 00000297 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\System Configuration.lnk from store
2022-03-07 13:05:54, Info CSI 00000298 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Accessories\\Snipping Tool.lnk from store
2022-03-07 13:05:54, Info CSI 00000299 [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\dfrgui.lnk from store
2022-03-07 13:05:54, Info CSI 0000029a [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\Performance Monitor.lnk from store
2022-03-07 13:05:54, Info CSI 0000029b [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\Resource Monitor.lnk from store
2022-03-07 13:05:54, Info CSI 0000029c [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\Windows Defender Firewall with Advanced Security.lnk from store
2022-03-07 13:05:54, Info CSI 0000029d [SR] Repairing file \??
\C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Administrative Tools\\ODBC Data Sources (32-bit).lnk from store
I forgot about powershell being missing. It was definitely one of the ones that was missing.