Actually, I didn't finished the eMMC defragmentation, I got up to 76% and gave up on it then I formating the drive instead and it makes the drive accessible much smoother than previously. I got less lag when opening files and folders. It was struggling and laggy to read from the drive.

I think I have wasted around 2000 write operations to the life span of my eMMC. Luckily it didn't finished so that wasn't so bad.