There could actually be a problem, depending on the size of the hard drive. You plan to use the machine under Win 98, which does NOT have support for something called "48-bit LBA". That is necessary to use any hard drive over 137 GB (by the maker's count, or 128 GB by Microsoft Windows' way of counting). So IF your newer HDD is over that size you have a problem. Otherwise don't worry.
Even if you were to upgrade your OS to Win XP there might still be an issue for large hard drives, either from the version of XP you use, or from the ability of the machine's motherboard to handle 48-bit LBA. But again, if the drive is smaller than that, it does not matter.