There are some edge cases that invalidate the flattened indexes, that are not accounted for. One is what happens when a pipeline transitions from non-JCas to JCas generators. Any flattened index built before this transition will have the incompatible kinds of Java Cover classes.
The other happens within a PEAR context - during that part of a pipeline, the classpath is altered, and the PEAR could be redefining the Java cover classes.
There may be others. For now, because measurements in real-life situations didn't show much if any improvement, the fix is to disable this feature.