I tried answering a question on this but had to create a new contribution.
I wanted to execute a SUBST (yes I know the pros and cons) and have it on boot up.
I found a simple way to set/edit autoexec.bat is to place it in this folder:
C:\Users\username\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Startup
This avoids issues with Win 7 or Win 10 deleting/hiding an autoexec.bat in the root C:\ drive.
I find the autoexec.bat file runs about 10 seconds after the start menu appears.
HTH.
Windows just runs anything it finds in there, pretty powerful if you ask me. Note this is after startup, not during startup, like autoexec used to be 🙂
And if he is deleting the file still, just rename it (with an executable extension of course).