[LoopFlatten] Mark inner loop as deleted

If a loop is flattened, the inner loop is removed and the LPM
should be informed of this fact, so it can invalidate associated
analyses. To support this, we relax an assertion in LPMUpdater to
allow invalidating non-top-level loops when running in LoopNestMode,
as the pass does not know how exactly it will get scheduled.

Differential Revision: https://reviews.llvm.org/D111350