Search the forums - this is a very common issue. This is why.
1. Install win98 on first partition - get win98 boot sector in first partition.
2. Install win2k on second partition. Win2k copies the win98 boot sector to a file which it writes to first partition. It also makes first partition win2k boot sector (includes files ntldr, ntdetect.com and boot.ini). Boot.ini contains your dual boot menu - uses boot sector file to load win98.
3. Reinstall win98. Makes win98 boot sector in first partition again (ie, removes win2k boot sector) - so you've lost dual boot.
I would recommend use of a third party boot manager which allows both operating systems to be independently installed, so you can reinstall one without affect the other (
is the one I use - its now free for personal use).
To re-establish your dual boot (or get access to win2k) - several options:-
1. You can create a 2k boot floppy which will enable you to access your 2k installation. You'll need a clean formatted floppy disk, and files ntldr, ntdetect.com and boot.ini. If you just reinstalled win98 without formatting, these files will still be in the root of your C: drive. If you didn't, the first 2 are on the win2k install disk (in \i386), and you can create the boot.ini using a test editor. Just paster the following and save as boot.ini:-
[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(2)\WINNT
[operating systems]
multi(0)disk(0)rdisk(0)partition(2)\WINNT="Microsoft Windows 2000 Professional" /fastdetect
This will boot into your win2k (so need floppy to boot 2k - otherwise will boot 98)
2. If you reinstalled 98 on top of itself, so files still in root of C: you may be able to re-establish the dual-boot using win2k's recovery console (fixboot command). If you do this, you may however find that the 98 menu option doesn't work. Would then need to go to option 3, after re-establishing win98 boot by booting from win98 boot floppy, saving the file msdos.sys (in root of C

somewhere, typing sys C:, then replacing msdos.sys with saved version (will need to run attrib to get access to msdos.sys in dos mode).
3. Using boot-us (assuming you reformatted C: before reinstalling). Copy the ntldr, ntdetect.com and boot.ini (as above) into root of your D: (win2k system) drive. Run recovery console & use fixboot D

. Boot into win98 & install boot-us - then use it to set up boot menu for 98 & 2k.
PS. To use recovery console, boot from win2k CD, choose repair, then recovery console. You'll need administrator password. Type help for list of commands.
Hope this helps - gone on a bit!