I think it depends on how how you handled Lucia originally - did you sleep with her at their home, primarily. I've done a few save files to experiment after having this exact issue, and I believe that's the key. Maybe Runey'll respond with more/better info.
never heard of a cheat code changing felicity and emma relationship, to be honest I've found and actually used the code "truestory" to start the 2 Lucia events. I know the code because i'm in runey's discord and he specifically wrote it in the FAQs
Oh? Maybe it changed sometime in the last couple updates. I got my info from the FAQ too, bout a year ago, bit less maybe. Plus I can confirm it does change how Felicity and Emma talk; I clearly recall old save files where they said "Clone", after using the cheat, "Twin".