Creatures Caves

The x-ray only kind of guesses which organ is which by what order they have in the genome or else by the 'sequence number' in the gene description I think... where is your new gill organ and what sequence or organ number does it show when you look at it in the gene list? (there are sort of gaps in the sequence numbers of the 'normal' organs, which your new organs might have been snuck into by the gene editor... if left alone, this could confuse the x-ray as to which organ is which and kind of push things down in the list)

I'm guessing that your timeline organ is not really dead, and what is really dead is your gills... at least, it seems to me the most likely explanation of why an emitter in the gill which is a carbon copy of a working emitter would not be functioning (though they could also just have a too-slow clock rate in the gill too, either from its settings or from a receptor slowing it...) Still, were the timeline organ really dead, I would think they would become immortal to aging, and as you say these have not stopped aging. (though I'm not absolutely sure they would become immortal just from that organ dying, I haven't tested that... but from what you are saying, you also have not made any changes to it that could possibly make it die any faster anyway... which is why I am thinking it's another organ that is really dead...)

Anyway, to start, I'd set all the organ settings for the gill to be the same as the lung and pay close attention to the loci that any receptors in there are attached to. Make sure the organ gene properly switches on at the right time too and that 'variant' is set to 0 for it.

Then, since the 'timeline' organ might have been pushed down in the list, look very closely at the organ or two directly BEFORE the timeline organ (both in gene order AND also organ/sequence order) for any issues with biotick start or anything that might be killing those organs, any emitters or receptors that can cause it damage, stop its clock rate, or age it prematurely, etc... Pay close attention to any organs you made any changes to... Your issue might even be complicated by another organ entirely... The skin organ for example is usually before timeline organ in the genome, and can also suffocate them (at least TWB), under certain circumstances, after it dies. With dead skin organ, it will stop them from being able to sweat, in which case most will eventually overheat, dehydrate, and suffocate... It's entirely possible that the actual overheating and dehydration that stops them from breathing doesn't manifest until they get somewhere warm though. So, if you don't find the answer in the gill, check the water, 110, and hotness levels in them as well when you see them unable to breathe.