There are numerous variables so it’s hard to make any useful comment. What are the seeds? Why do you use a paper towel to germinate? What are the growing conditions ie temperature, light, moisture, etc.? Possibly you just damaged the radicle with all the moving about. When you dug it up did it gave a healthy radicle? To be honest I think you’d do better just to sow the seeds in the ground or medium, as appropriate, and leave them in peace. Less work for you and less disturbance for the seedling.

I have simply found that germinating first in the moist paper towel speeds up the process. Yes, the radicle looked very healthy, long and white. I have never had this issue before; zero light, moist soil (not overly wet). I agree risk of damage to radicle upon moving from one medium to another, but it’s weird that it started to grow again and then just stopped; I wouldn’t have expected it to grow at all if I had damaged it in the process of moving.