Tier 2 to ILR (very confused situation )

I have been working on Tier-2 on the grant from Innovate UK(https://www.gov.uk/guidance/knowledge-t ... w-to-apply). This role is a partnership between University and company. The University has sponsored me the tier-2, they take care of the payroll etc but I work full-time at the company(this is how KTP works). My company is making me permanent after this role. Here comes the confusing part:

End of tier-2 Jan 2020
Due for ILR - Nov 2019

University cant give me a letter stating I will be employed for foreseeable future(but happy to explain the situation), As by end of the grant they no longer will employ me. But the company is happy to write a letter stating that I will be employed for foreseeable future. will these letter suffice?

Or

Should the company get tier-2 sponsor license, then I change and then get a letter before ILR?

Many thanks
Sat