Try using this script which should move every text box to a new layer. Before running the script, manually remove any text boxes from your master pages.
newLayer = app.activeDocument.layers.add();
To create the script open Adobe ExtendScript Toolkit. Create new file. Paste the code as it is (remove extra row so you will only have two). Save file to
Program Files\Adobe\Adobe InDesign\Scripts.
In InDesign open script tab (Window → Utilities). Your new script should be visible in the 'Application' folder or below. Double click to run it.