There is more than one way this can be fixed, but Scitech recomended this:
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From snapos2.pdf:
Restoring Your System in Case of Failure
If SciTech SNAP Graphics does not correctly boot on your system, you
can easily switch back to the GENGRADD drivers to boot your system to
a workable state again. To revert to GENGRADD, do the following:
1. Boot to an Alt-F1/F2 command prompt mode
2. Edit CONFIG.SYS file and change
C1=SDDGRADD
to
C1=GENGRADD
3. Delete or rename the x:\os2\svgadata.pmi file
4. Reboot your system.
If that fails you will need to revert to VGA mode and reinstall your
prior display drivers (Alt-F1/F3 for Warp 4 and later systems during
bootup).
Note: Even if you use GENGRADD, you should still be able to run the
SciTech SNAP Graphics command line utilities, provided that you didn't
remove any of the SciTech SNAP Graphics files or the
DEVICE=X:\OS2\SDDHELP.SYS line from your CONFIG.SYS.
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Also, You might try fastest way of reset to 640x480 without going to VGA by wiping your settings in \os2\drivers\snap\config. Smart way is that You backup 'em first (copy to new name, then delete).
Also I presume that You have default statement in config.sys SET RESTARTOBJECTS=YES, this can cause similar problems in future: I recomend that You change this to SET RESTARTOBJECTS=STARTUPFOLDERSONLY. This way, only programs that are in startup folder will automaticly start when boot.