Win98se Start-up Error: File Not Found

Hi! I have a Win98SE minitower at my mother's house. It has a lot of issues, and two of them are a file not found error loading a driver from Open Watcom and too many programs opening after I log on. I remember finding the former reference in a portion of the system registry about which I don't know, and to solve the latter, I need to uninstall some programs. The reason for the former is that the program is on a flash drive that acts as a second hard drive. Will simply removing the reference cause any other problems?