Sorry to hear your experience. I can imagine how frustrating and worrying it must be.
Under normal circumstances it's often tricky if they will accept "out of time" applications, and in principle it is entirely discretionary.
However your case is different in that your application remains 'in-process' and you have been told to re-apply.
You applied correctly and until such time as any decision is taken about the granting of ILR then FLR status remains in place.
Just remain calm, there is no chance that anyone will have to leave UK
