" How do I reset it or switch to 640x480? In Windows 9X there is a safe mode, does OS/2 have a safe mode?"
Its been a long time since I dealt with Warp3, but I think Connect had the following option that was available on Warp4. On boot when you see the OS/2 White Boot rectangle in the upper left corner, hold Alt and press F1. That will bring up the boot recovery menu. Set display to VGA should be on there.