Bench migrate losing data after update to v13

So, I have updated ERPNext from v13 beta to v13.5.2, and whenever I run bench migrate, the changes I made (custom scripts and print format list) after the update are being lost.

What is the problem here? If I made any changes to the system on v13, and run bench migrate, the changes should still be there right? Looks like I am losing those changes on bench migrate.

If someone knows what is the reason behind this, and how to fix it, please let me know!