When I installed MX-linux on one of my old dual boot systems, GRUB didn't see my old windows partition. But I could boot MX-linux.
I installed MX-linux in my old ubuntu partion. I formatted the whole ubuntu partition (removing ubuntu). Ubuntu had no problem on my system.
I expected that a simple Mx-boot-repair would solve the issue, but it didn't happen.
I had to do manually do a sudo update-grub to make it work.
I am still confused why mx-boot-repair couldn't do that.
So, maybe you can try a simple : sudo update-grub
After booting your MX-linux on your hard disk via your USB stick.