ILR Via Tier1+Tier2 (contracting through agency on T1E)

[avaixhah]

Hi All,

I am posting on behalf of my friend. Please advise on the following query.

I was granted Tier 1 Entrepreneur in May 2014. For that visa I used a Contract through an agency which I also submitted along with my visa application. The contract did include “Contract for Service”. Then I switched to Tier 2 in March 2016.
But as HO clearly mentioned in updated rules (July 2014) that HO does not allow this type of contract/working through agency on T1E.
If anyone can please advise on following 

Did the updated rules applied to me?  

If yes to 1, will it affect my ILR application? 
Thanks in advance.

[zimba]

Under Tier 1E rules, contracting in capacity of an employee was never allowed. If HO believes that you were in breach of the conditions of your stay, then that can affect your ILR