ILR Due in Jan 2020 first week - Need advice on my case

[raj0419]

Hi All,

I need very genuine advice from all and experts please.

I came 2015 Jan in Tier 2 visa I worked continuously till Oct 2016 with the same company. But this company sponsor license revoked in 2016 Jan and then company tried to produce documents and to home office and too fro process going on and finally in the appeal comes revoke the license in Oct 2016. I switch to another company on Tier 2 from September 2016 onward and continue working April 2017. but in financial year 2016-17 I got bonus from my previous first company 10k which includes (my 2 months holiday pays, overtime, bonus, other benefits).
From June 2017 again I started working in new company till on Tier 2 and as per immigration rule I am going to eligible for ILR in end of December or first week of Jan 2020.

Problem is I got letter from HMRC simple assessment in 2019 feb for the year of 2016-17 for the tax I own around 6k, then same day I stared verifying my salary and payslips and records in my personal tax account in HMRC site I found a duplicate entry in my simple assessment letter but I am not able to see in login account. Then with in next 2-3 days I sent my payslip, P45 and cover letter to HMRC for proof and explanation for this blunder and several calls. Then with in week time they send again a letter says we notice this error of duplicate entry happened and advice to tell company to update in HMRC system. But unfortunately the first company is dissolved so I don't have any contact to them which I explain to HMRC fully. They said you don't worry we will contact whoever dissolved this company this process continue 7 months. In between I called so many time check updated then I had chat with HMRC people they advice not to pay and wait for our decision for rectification and some said you can pay and wait for refund. So I had chat print for safer side later any issue where adviser says not to pay anything and wait. But again after few 1 month this is not resolved I decided to finally paid 6k amount to HMRC and waiting for resolved this issue and for my refund. Then in Sept they refunded full amount which I paid and recalculated my tax from 2016-17 years and put 2k tax you own and they said you don't need to pay we will deduct from financial year 2019-2020 from your salary. But I need to clear this as soon as possible but online there is no way and even If I pay by cheque then I need charge ref number. So when I am applying my ILR in December or January is there any chances for reject by saying you have tax pending to pay HMRC or any other clause where I am failing. Please advice