So when you made your MC application you would normally be applying as either a late submission or a non submission.
If it was for a late submission, normally the late period is already set, e.g. up to 7 days late. Or it sounds like 5 days at your uni. This is written into all assignment briefs etc.
You would know this when you made your application so it's not clear why you have managed to miss this deadline.
As it sounds like have missed the late submission deadline, you have probably by default become a non submission. You will now have to ask to formally request that the MC application be changed to a non-submission. Usually you can't do this yourself, you will have to go back to your programme administrator and ask them to contact the MC reviewer to reconsider your application.
I can't comment on the specific regs at your uni, and there may be specific rules about failing core modules that make this a worrying situation but normally the worst thing that happens in a situation like this is that you have simply failed the essay and therefore the module and will be set it as a capped resit over summer.