My peo appointment is in 10 days

I recently found out that when i switched my post study to HSMP my accountant who has now closed the company and ran off never checked my accounts properly and some of the tax is still outstanding, however this was back in 2011. In 2012 before my extension on HSMP i converted my visa to spouse and have been on it since.
My spouse is British national, and we have a baby together as well.
Now, I have spoken to this new accountant, and he says he has sent the details to HMRC and is awaiting a reply from them on the outstanding amount and any fines etc. on it. He says this can take 6-8 weeks. I told him my PEO is in 10 days he says he will write a letter confirming that we are in touch with HMRC and the balance will be paid in installments in due course. Since i have been told after the ILR i still need to pay the tax because it all gets checked again before they give you the passport.
My question is, I will pay this tax, but i only have 10 days left, and since i was on spouse visa last will the tax still get checked. I was only on HSMP for less than 2 years. I left work after a year because i met my spouse and relocated. Is it still relevant.
Freaking out here!!, hope it makes sense will be waiting for replies

Thanks