Wrong Index used on AS400

We have been running the R077011 - Tax History Integrity for years.  It used to run in 15-20 minutes on the AS400. Recently we added custom indexes to F06166.  It used to have 7 indexes , now it has 11 indexes.  The R077011 references using Index 6 of the F06166 when doing a Select Fetch Next.  We notice on the AS400 when it is running that it is now using Index 9. It now runs in 3+hrs.  So it appears that we know what the problem is, but we don't know how to fix the problem.  We do regular deletion of SQL packages.  What could have caused