Sorry for the delay in getting to this!
There was an issue where the text label in the tree was not updating its color to match the visibility dot. This was only a visual thing, it wasn't a problem otherwise.
I haven't been able to reproduce the dots disappearing completely. Do you have steps for that?
As for the left eye being in the wrong place, it is imported into Spine as it is in the JSON:
"left_eyeball":{
"[snip]/left_eyeball":{
"width":55,
"height":52
},
"[snip]/roll/1/left_eyeball":{
"x":25.66,
"y":102.01,
"width":55,
"height":48
},
"[snip]/roll/2/left_eyeball":{
"x":23.54,
"y":77.95,
"width":49,
"height":33
},
"[snip]/roll/3/left_eyeball":{
"x":22.49,
"y":70.03,
"width":45,
"height":30
},
"[snip]/roll/5/left_eyeball":{
"x":20.51,
"y":155.01,
"width":46,
"height":30
},
[snip]
I'm afraid there isn't any more information about the eye being in the wrong place, so we can't move it back to where it should be. Do you have a Spine project where the left eye images are not moved up? When you export that to JSON and then import it again, does the eye move up?