Update Counters 
The update counters section lets you ensure that counters such as number of replies in an issue or the number of issues in a project are correct. This is a maintenance section. You do not need to run either of the options here unless you suspect that the counters are incorrect. They should remain correct during day-to-day use.

There are two counters that can be rebuilt:
User Contributed Notes: Update Counters Add a Comment