As it turns out if I just changed the Username in /etc/passwd
(*column 1) it seems to have worked just fine. I believe MSYS uses the SID of the Windows user, which you can see in the 5th column of
passwd, which is the
GECOs column. MSYS uses this SID to create the UID of the user. So even if you change the username to something else it still keeps the same UID, which I believe will keep the same permissions of the Windows User.
Here is where you can find the commands to create "/etc/passwd" and "/etc/group" using mkpasswd/mkgroup, if passwd & group do not already exist:
https://cygwin.com/cygwin-ug-net/using-utils.html
*This link had a good explanation of the Windows SID and how MSYS uses it to create the UID:
https://cygwin.com/cygwin-ug-net/ntsec.html#id317355
This also contains some info that helped me out:
https://www.cygwin.com/ml/cygwin/2006-07/msg00784.html
Thanks,
Matt