Edited to fit in header... the actual message reads..

"Bloodmoon.esm is required for this file to be loaded, and it has changed since this file was last saved. You might experience problems with the game"

I see this message when activating the Oblivion style quiver mod in my Morrowind launcher... What does this mean and how do I avoid said problems? (being an error message when I boot the game)

Open Wrye Mash and go to your mod list. Scroll down, and you should see that the checkbox next to that mod is yellow. Click on the name of the mod so that the masters display in the lower right box, then click within that box so that every checkbox for the masters displayed within turns green. Hit Save underneath the box, and the checkbox next to the mod in the mod list should go green. Do this for every mod in your mod list that has a yellow checkbox next to it, and you won't see that message again.

I dont have wrye mash, is there another way to disable the message?

The error comes from using a different version of Bloodmoon than the modder did.
This is very common and completely normal. The error is also harmless, although very annoying.

You could load the mod in the CS, save and exit, but that will add the evil GMSTs and also change the time stamp of the esp and therefore change your Load Order.... so you would likely want to correct that with Mash too.

Get Wrye Mash. It's very powerful and handy tool to help keep your modded game happy.
Especially for players new to modding, it's essential.
The http://www.gamesas.com/topic/1106095-wrye-mash-stand-alone/ is the easiest to install/use.
http://www.gamesas.com/topic/1449775-wrye-mash-thread-6/ is the Mash thread, for any help you might need.

Wrye Mash is also needed to make a MashedList.esp which is something you'll want if you're going to be using mods that alter leveled lists, (and many do)

I'm just curious...

Let say I just did that can I backup the *saved* esm/esp and later use it for the actual mod in question I mean if I need to save master list in Wrye Mash then replace the original plugin with the re-saved plugin in the archive for later use. Are the changes permanent?