First, make sure that another instance isn't running. A command something like this should do the trick:
ps aux | grep fill_summary_index
If it's not, then check for a temporary file in $SPLUNK_HOME/etc/apps/Catch/log/. If you have a "lock" file in that location, you should be able to remove it and then run fill_summary_index should work after that.
I believe the limitation is running on one instance of fill_summary_index per splunk application.