LY6 installed into a L96 2010 3500

[Dutchtouch]

So I have started work as a fleet mechanic for an all Chev line up of trucks.Truck came in both LT trims pinned lean. checked it all out and found through previous R.Os that it had an engine installed out of a 2009. Thus making it a LY6 and in turn has the 2010 requiring the L96 I came onto this because I changed fuel rails because old components were there and I noted the part number difference between the two. My question is there any way out of this or is the variable timing and e85 technology leaving me with no other options but to get a L96 back in er?