There are three options to workaround this problem:
Option 1: Recreate the index.
Backup and remove directory "/APM_HOME/traces/index" and restart the Enterprise Manager to regenerate the index directory.
Option 2: Re-index the currently traces directory by using ReindexBuilder found inside APM_HOME/Tools.
Run <APM_HOME\tools> IndexRebuilder.bat APM_HOME\traces.
Option 3: Delete all traces folder if losing traces data is not a problem.
Stop all Enterprise Managers to perform above activities.
Start again after all of the above activities done.