ILR Tier 5 to Tier 2

[DrSai]

Hi All, Happy new year. I am doctor with a permanent contract with NHS. I came to UK on tier 5 in 2011 and returned to home country in 2013. After my contract ended before returning to my home country I submitted my p45 to HMRC and received tax rebate for that financial year as I left job midway in the financial year. I wasn't sure of returning to the UK at that time (family issues). But I decided to return to the UK the same month I left UK so got a job and returned to UKon a tier 2. On my return I informed HMRC of change of circumstances and I am paying the tax refunded in instalments.I will paying altogether this month. I will applying for ILR in Aug 2018. I am worried that HO can see this as a deception. Please advice.
Many thanks.