Once I used Nestedset behavior for Doctrine, Symfony in a project, and faced issue with broken indexes. (You can read how Nested Set works here). This happened because low-level MySQL query executed during migration, and because of this Doctrine events responsible for refreshing indexes was not executed. To fix that a Symfony Command was written, which refreshes indexes. This is just example. Better way is to move this code to the service and add one more migration which will refresh indexes. Here is just simple example how this issue can be solved.
Argument of the command is an entity to refresh.