Your post is confusing. However:
a) If the skin works on Matrix, it works on Matrix. If you manually upgrade from Leia to Matrix you still end up on Matrix. There is no reason why you cannot remove the Leia version of the skin (reverting to Estuary) and then update and install the Matrix version and start using it.
b) If you backup a Leia install and then do a clean Matrix install and restore the 'Leia' backup you pollute the Matrix install with Leia stuff. You will need to a selective restore of only the things that don't cause conflicts (e.g. add-ons).
c) LE is packaged with the entire OS in two files: KERNEL and SYSTEM. This means you cannot update "Just Kodi" because our OS packaging dictates that you update everything at the same time .. but if you are self-compiling you can update to an image that contains only whatever Kodi change you want to make. If you are thinking to use the Leia OS base that you customised but with "Kodi Matrix" .. it's not impossible but nobody around here is likely to spend a month on forum posts to explain how, so you either know how, or it's best not to ask.