Overstayed because of delayed response from home office

I applied for a tier 2 dependant which was refused because I had a pending appeal which wasn't fully withdrawn and my main applicant did not meet a criteria so she was refused as well. But the home office did not get back to me after knowing my application won't be treated.
They only replied me when they where ready to reply my main applicant which was 42 days later by then I had overstayed by over 28days.
I was ready to make another application but had to wait for the response from the last application.
It's quite understood that my appeal was not yet withdrawn and so my application was void but the home office contacted me twice for other reasons without informing me I had 28 days to make a fresh application.
Am now regarded as an overstayer. I have 2 children here almost 5yrs and a year plus. I got married here but need a good advice because I have been asked to start signing with the immigration already.

Kindly advice me pls.

[deleted]

If your appeal is still pending, then it's unlikely that you are an overstayer.