HMRC No Employment traced - ILR

[icon3001]

Hi All
Got In-country HSMP in Dec 2007 - Dec 2009 (2 yrs) using income from Self Employment (Director Limited Company 100% shareholder)

Paid All HMRC taxes for that year
then next year late submitted accounts and then paid no corp taxes.

Got Tier 1 (General) - Jan 2010 to Jan 2013 - using Self Employment again in similar capacity as above (ie Director 100 % shareholder)

Closed company and HMRC has the following records (got the 5 yr history from HMRC)

2007/08 Limited company earnings recorded
2008/09 No employment traced (though I submitted company annual financial accounts)
2009/10 No employment traced
2010/11 No employment traced
2011/12 Permanent Job earnings recorded (started working as permanent in a company)

For ILR I can score points using permanent job salary only.
Do they ask for previous HMRC "No Employment traced" records?

Looking for expert ideas please.