Hey,
I'm experiencing a similar issue (can't find applications & many folders), but this is on Catalina.
I've ran through all the troubleshooting steps. Here's what it spits out when trying to locate an app:
Check mdls file metadata...
❌ macOS metadata missing essential items
kMDItemFSContentChangeDate = 2020-08-20 12:30:11 +0000
kMDItemFSCreationDate = 2020-08-19 07:48:18 +0000
kMDItemFSCreatorCode = ""
kMDItemFSFinderFlags = 0
kMDItemFSHasCustomIcon = 0
kMDItemFSInvisible = 0
kMDItemFSIsExtensionHidden = 0
kMDItemFSIsStationery = 0
kMDItemFSLabel = 0
kMDItemFSName = "Brave Browser.app"
kMDItemFSNodeCount = 1
kMDItemFSOwnerGroupID = 80
kMDItemFSOwnerUserID = 501
kMDItemFSSize = 1
kMDItemFSTypeCode = ""
---------------------------------------------------------
If my indexing is broken - can you suggests ways to fix it? Thanks.
Joel