Note that at this stage, this report is somewhat based on guesswork from the symptoms of the bug - I have not fully investigated the cause.
As you will know, if you load a level in NL but some pieces are missing (most often due to needing a style you don't have), those pieces show up as a ? icon in-game. The bug that arises from this is, at least in some cases, it'd appear that cleansing such a level results in references to the fallback piece, literally being written into the output level file - as if the missing pieces were actually aliased to default:fallback.
This should not happen - NeoLemmix should either refuse to cleanse levels where a needed piece is absent, or else should preserve the original reference (while still correcting any that it can correct). My preference is slightly towards the latter.
I consider this bug to be reason to look at a 12.12.2 update, although not promising any timeline on that.
