Hello,
That is very weird since updating was always smooth from any version and havent been yet reported such a behaviour.

Check 1: I suppose your custom tasks were not in the NodeCanvas folder that you deleted (stupid question I know)
Check 2: Did you reload your scene or reopen Unity after deleting old folder and importing the new package?
Check 3: Do your custom task scripts have the same name as the class they implement?

What was your last version from which you upgraded from so that I try exactly that upgrade as well.