I learned back in my Win 3.1 days to make backups of win.ini, system.ini, config.sys and autoexec.bat files as Windows breaks so easily. Have you checked autoexec.bat? Mine,
@ECHO OFF
ECHO.
PROMPT $i$p$g
REM SET DELDIR=C:\DELETE,512;D:\DELETE,512;E:\DELETE,512;F:\DELETE,512;G:\DELETE
,512;H:\DELETE,512;K:\DELETE,512;M:\DELETE,512;N:\DELETE,512;O:\DELETE,512;P:\DE
LETE,512;Q:\DELETE,512;R:\DELETE,512;S:\DELETE,512;T:\DELETE,512;W:\DELETE,512;X
:\DELETE,512;Y:\DELETE,512;Z:\DELETE,512;
SET WIN3DIR=W:\OS2\MDOS\WINOS2
PATH=W:\OS2;W:\OS2\MDOS;W:\;W:\OS2\MDOS\WINOS2;W:\sys\MDOS\BIN;W:\TCPIP\DOS\BIN;
LOADHIGH APPEND W:\OS2;W:\OS2\SYSTEM
SET TMP=W:\var\temp
LOADHIGH W:\sys\MDOS\BIN\2GBFIX.COM >NUL
LOADHIGH DOSKEY FINDFILE=DIR /A /S /B $*
DOSKEY EDIT=QBASIC/EDITOR $*
SET DIRCMD=/A
SET TEMP=W:\OS2\MDOS\WINOS2\TEMP
SET ETC=W:\TCPIP\DOS\ETC
Adjust boot drive letter.
Today I would back up\os2\mdos before doing any test installs. A simple zip works.