initializing my hard disc - what???

Since i upgraded the OSX partition of my hard disc to OSX10.3.9 the other partition running OS9.2.2 does not recognise the OSX partition at all - it's as if I only have a hard disc half the size and can only run OS9! when i boot up a message comes onscreen saying "computer cannot read this disc, do you want to initialize this disc? with the option of 'Mac Standard OS 4.7GB' or 'Mac Extended OS 4.7GB'. Obviously the 4.7 refers to the fact that each partition is only 4.7 gygabytes but I'm not sure which ooption to choose OR MORE IMPORTANTLY should I actually initialize at all or is a serious error in progress? Please avise, I don't want to lose my OSX facitlity...