Where did Linux go ?

Win 98 has started to lose .exe files, one of which was for ftp. My friend set up my Compaq so it asks you which system you want to run, Linux or Windows. I reloaded 98 in an attempt to get back the ftp .exe files, and now it will not ask you which system you want to run, it just boots Windows. But the C drive has the same amount of free space, so I think Linux is still on there. How can I reconfigure so it asks me which system to run ?