On my personal server I have a GIANT city map that I need to plot a absolute TON of waypoints. TO emphasize my point I took a screenshot: Is there anyway I can save my waypoints when I update?
even if you happened to uninstall the mod for another mod and then started to use rei's minimap again you would still have all of your waypoints mapped
I think Rei's Minimap stores your waypoints and other information in a separate folder from the mod. When you update the mod, it should auto-load the waypoints. If not, you can just try manually putting the old files into the new folder. But yes, it's always a good idea to keep backups.
The folder which contains the data associated with Waypoints in Rei's Minimap is found "%AppData%\Roaming\.minecraft\mods\rei_minimap" so long as that folder is never deleted you will still have all your waypoints when you update your client or the mod version. If you switch computers and need the waypoints copy that folder... Also with that much valuable information I would suggest that you keep and active backup of the folder... Hope this information helps
if you need help installing -> click here http://youtu.be/AMLjUDBXjCY Also if you go into your mods folder all your waypoints will be saved in a folder called rei_minimap copy or cut this folder from here and paste it into your updated minecraft mods folder once you have the update for rei's minimap installed and working.