If OneDrive is install per machine and autostart set via REG ADD HKLM\Software\Microsoft\Windows\CurrentVersion\Run /v OneDrive /t REG_SZ /d "\"C:\Program Files\Microsoft OneDrive\OneDrive.exe\" /background", is there a way to use WEM to prevent it from running on published app, when customer uses both session desktops and published apps from same session hosts? My 1st thought was to change the run to be HKCU and then i should be able to target the key based on User SBC filter/condition but wondering if anyone has another solution. .

pretty sure that would be the only way. I asked Citrix about this in general since they made the shift to shellbridge for published apps, they basically said there is no native way to do it if the vda is serving both pub apps and pub desktops. I think your idea on the SBC filter would work.