Try putting this at the end of your batch file, and also directly underneath your FreeFileSync command, if those two things are not identical:
if NOT %ERRORLEVEL% == 0 echo "errorlevel not zero"
If that text then shows in the UC4 report, there is some error happening. Maybe it syncs all of the files but one or there is some other error in between? It's sometimes easy to miss for tools that output multiple pages of report. The above is how Automic checks for any errors for Windows jobs, it's purely based on the value of %ERRORLEVEL% (at least in the default template for Windows jobs).
I'd not change the status "dynamically" in Automic if there is a legitimate reason for the tool reporting an error. If you do this, you might risk missing any potential, actual problems.
Hth.