Question: If I run win98 setup on a pc, already running win98 without formatting the hard disk, will it re-write MBR or will the MBR remain as it is?
Answer: It will rewrite the Master Boot Record. If you had a custom setup there you will need to reinstall that after reinstalling Windows.
Where you have several primary partitions configured on the drive and are using a boot manager attached to the Master Boot Record to decide which of the primary partitions to boot, installing any version of Windows into any of the partitions will overwrite the MBR with a reference to the version of Windows just installed and you will need to reset the MBR to point it back to the boot manager in order to recover access to the other operating systems. If it isn't just a reinstall of what was already there then you would also need to add the new operating system to the boot manager.
This article written by Stephen Chapman, Felgall Pty Ltd.