OK, so... here's where I'm up to:
Thanks to namida, I have an extraction tool that can generate LVL copies of the Amiga levels by decompressing emulation savestates - genius!
Furthermore, thanks to geoo, I have a full set of already-extracted Amiga LVLs, which saves me having to create 120 savestates and extract them all manually.
I did a few manual extractions in order to compare the two by opening the respective LVL files in the NL Editor, to make sure they're the same. Indeed, both the savestate extraction and the LVL from geoo's zip folder looked like this:
As you can see, some of the water graphics are missing. It's good in the sense that, at least I know that the zip folder from geoo contains the exact files I'd obtain by extracting them manually using namida's tool. So, that puts the conversion project a few steps forward.
I then discovered that opening either LVL file in the 1.43 Editor yields the following:
So - all of the water is there! This indicates that the files themselves do indeed contain the necessary data to generate the objects. However, it also confirms what namida said about new formats disregarding objects that are in a certain "slot", as the LVL file marks these as "fake".
All I have to do is open the files in 1.43, save it as a new LVL file, and then open it in the new Editor - everything is there, intact!
This means that no manual editing is necessary, which is great! However, it would take quite a lot of time to open each file, save it, re-open it, and save it again.
So, thankfully, namida then provided a magic version of NeoLemmix which doesn't disregard "fake" objects. By using NL's F8 "Cleanse levels" feature, I was able to obtain a full pack of completely processed NXLVs with all terrain and objects intact!
So, once again:
thank you, namida and geoo! I can now start work on the newly restored conversion of
Lemmings.