I managed to recreate your project and I can see the issue. I think I can see two solutions:
#1 Duplicate your text layer and have the cursor on this one (and not on the other) then either use a strobe effect or keyframe the opacity to blink the duplicate on and off
#2 Use a shape layer to make the cursor. And link its position to the text using this expression:
var Y = thisComp.layer("Text file").transform.position[1]+effect("Y Adjust")("Slider");
var X = thisComp.layer("Text file").transform.position[0]+thisComp.layer("Text file").sourceRectAtTime().width+effect("X Adjust")("Slider");
[X,Y]
I added a couple of sliders just to make it easy to properly align the cursor, but sourceRectAtTime does the hard work here.
I used loopOut(“pingpong”) to control the opacity:
if (thisComp.layer("Text file").effect("Cursor On/Off")("Checkbox") == 1) {
loopOut("pingpong")
} else {
0
}