-The bottom of the caves had almost no silt, and it would be very really hard to intentionally silt out the cave
The silt on the bottom is not the only thing you must worry about. Simply scraping a wall or rock can silt the place out. I have been lost in a silt out in Mexico that came from someone kicking the wall in a small area. Luckily I was able to find my way out and meet back up with the group. I had to deploy my safety reel and find the line. It's not a fun thing to do.
-Even in the cavern portion of these dives, sometimes it was not possible to see daylight
Then you were no longer in a cavern portion, you were in the cave.
-We weren't right on top of the lines all the time, sometimes we were quite far from them but they were easy to see anyways (amazing vis)
Not a good idea to stray from the line. Just because you can see a line one minute, does not mean you are going to see it the next. If you do not have the training to find a lost line, you could be screwed.
-On two of the dives I did a long time ago almost all of the dive was in caves, and in pretty tight tunnels, far from the exit, and a bit deep. (I had very little experience, would not do that again!!!)
I am glad that you "would not do that again". Your guide should have never taken you there in the first place.
I can not see how someone experienced like the guide, who has dived that cenote many times could get lost in it and find himself in an out of air situation. The dives are pretty short and shallow, and even with only one AL80 we could have done twice the same dive.
We don't know if he got lost, or if one of the tourists wandered off, or if the line was cut as some reports state. I am sure they were scared once their air started getting low. Then they sucked down the tanks even faster. It appears the guide and the female ran out of air at the same place, giving the look that they were sharing air. This along with the fact that the gentlemen had already died I am sure caused even more issues and panic.
To get lost for that long without finding a line seems to me pretty hard to believe. Even when far from the line I can't imagine a full cave diver would not find a line in one hour.
If you have never searched for a lost line, you can not possibly understand.
It's not like they were completely silted out either, or 500m from the exit. Also there are lots of air pockets where they could have tried to breathe from. The only thing I can imagine is that all of their lights failed and that they couldn't see the exit or the lines because they where either out of the cavern zone, or because of the low natural night at that time of the day.
We don't know if they were silted out. We don't know if their lights failed. Air pockets are not in every cave. They were found in the cave, not the cavern zone.