Manager becaome eligible (was limited) after Full Refresh

In our plan we have a group of managers with 2 assignments (primary and no primary). After starting plan primary one is elibile and no primary limited (managers have subordinates under second assignmnet).

In the plan we are using Employment Records to Use: Primary Assignment

After running Full Refresh of plan, all managers who were limited became eligible. Does any one know how to fix that? We can make those assignment ineligible but managers will still be visible in the plan (as limited they are not).

Thank you for suggestions