Yes you absolutely can delete them… just not from your ipad… if you add a marker track in your project (if it’s not up already) you can see each marker that you create from Cue IC Pro being added in your actual project. So you can add as many as you want on IC Pro and they will be shown in your project… you just have to actually delete them using the eraser or whatever within the actual Marker Track in your Project and IC Pro will delete them automatically.
Hope that helped a little!