I can feel for you. I used a blue chalk marker on some embroideries years ago. Put everything away due to moving and finally after so many years started unpacking some of the totes to see what was in them and found these embroideries with the blue markings still there. I serged the edges and put them thru the washing cycle to see if the marks would come out, even sprayed them with Spray & Wash. Some of the marks came out but most did not. Nowadays I put my marks just at the edge of the fabric to hoop it so it will either be hidden in the seam or chopped off. Have learned the hard way. I'm sure if I had removed the marks earlier I wouldn't have had this issue but time in storage made its ugly mark. Lesson learned.
Hope you find a way to remove them after all that work you put into it.