The issue there is whether, in order to get the VFR-only restriction on the current permit removed, you have to change the engine.
The last word is to come from the permit issuer, but yes, that seems logical.
Would have to make sure first though that your plane is certified or certifyable with both the non-certified and the certified engine. From the point of view of a certifier/permit issuer they are separate engines, after all.
I checked the Rotax 914 F/UL POH (1.4 – safety notice) and it doesn’t contain a restriction to VFR other than “always make sure, that a successfull no power landing can be made”. On the same chapter/page "For each use of….Night VFR, IFR…. °
This is after a revision of Feb 1st 2015, in the edition of Apr 1st 2010 there is a passage contained stating “The Rotax 914 UL (non-certified version) is restricted to DAY VFR only”
Don’t know about the LAA, but the engine makes no difference for an experimental. A certified engine doesn’t really get all that certified when mounted in an experimental. Fuel, cooling, carb heat, and so on also need to be taken care of, and there is no way to certify that (whatever certification should mean in this circumstance). The main question is really about how wise it is to fly with any SEP, IFR in the soup, and the soup extends downward below VFR minima. Also, in a Lancair, the chances of surviving (without serious injury) in an off field landing when the engine stops isn’t all that great even in clear blue skies. It’s the equivalent of driving off the road, into the woods, at autobahn speed.
A certified engine doesn’t really get all that certified when mounted in an experimental.
So it might well be, that common sense finally prevailed in this LAA-IFR with Experimentals-trial, given the fact that there ARE no differences between the certified and non-certified Rotax engines and the consequences of an engine failure in a SEP in IMC.