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Just for the record, I had exactly the same problem — and am glad I found my way to this discussion.  But I definitely did follow the steps outlined by @Vero above during setup.  My general preferences appeared to have been copied over, but not the folder I use for syncing.  Once I set that manually, everything was fine, but it didn't happen without my intervention.

Are your hot keys opening apps?  I too thought my hotkeys had stopped functioning when I upgraded to Catalina (which is what brought me to this page).  Eventually I realized that the hotkey tigger was fine.  It was Alfred calling the app that needed to be changed.  Apparently /Applications/Mail.app is now /System/Applications/Mail.app — at least that's what Alfred sees — and what was formerly /Applications/Microsoft Word.app is now /System/Volumes/Data/Applications/Microsoft Word.app.  All this apparently has to be manually changed in Alfred, workflow by workflow.  

(If this is not your problem, my apologies for intruding.)